Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The capital outlay and ability to train and retain skilled, multidisciplinary staff for a dedicated, high-throughput genomics facility is out of the reach of most organisations. Small-scale investment in genomics platforms in an institute or research group cannot deliver UK research ambition for high-throughput single-cell or population genome analysis.
The National Capability in Genomics and Single-Cell Analysis (NCGSC) (NC1) enables the provision of a dedicated, efficient, high-throughput genomics and single-cell analysis facility to support UK research communities, in collaboration with EI, or as a provider of services.
The NCGSC will provide access to new genomic technologies as well as bespoke bioinformatic and high-throughput lab pipelines with a focus on crop, microbial and non-model animal research. Driven by interactions on the Norwich Research Park (NRP), national and international research programmes it will deliver widespread scientific impact. The platforms complement the expertise of EI Faculty and supports the NCGSC to address genomic complexity in agriculture and food security. Links to the Norfolk and Norwich University Hospital and Quadram Institute Bioscience on the NRP will transition this expertise to bioscience for health, particularly in microbiome studies of health and nutrition.
This National Capability will tightly integrate with the national capabilities in the Plant and Microbe DNA Foundry (NC2), e-Infrastructure (NC3) and Advanced Training (NC4) to continue to provide end-to-end research solutions in genomics and single cell fields.
The National Capability in Genomics and Single-Cell Analysis (NCGSC) (NC1) enables the provision of a dedicated, efficient, high-throughput genomics and single-cell analysis facility to support UK research communities, in collaboration with EI, or as a provider of services.
The NCGSC will provide access to new genomic technologies as well as bespoke bioinformatic and high-throughput lab pipelines with a focus on crop, microbial and non-model animal research. Driven by interactions on the Norwich Research Park (NRP), national and international research programmes it will deliver widespread scientific impact. The platforms complement the expertise of EI Faculty and supports the NCGSC to address genomic complexity in agriculture and food security. Links to the Norfolk and Norwich University Hospital and Quadram Institute Bioscience on the NRP will transition this expertise to bioscience for health, particularly in microbiome studies of health and nutrition.
This National Capability will tightly integrate with the national capabilities in the Plant and Microbe DNA Foundry (NC2), e-Infrastructure (NC3) and Advanced Training (NC4) to continue to provide end-to-end research solutions in genomics and single cell fields.
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- Cytiva (Collaboration)
- Canterbury Christ Church University (Collaboration)
- Helmholtz Zentrum München (Collaboration)
- University of Oslo (Collaboration)
- University of Iceland (Collaboration)
- Uppsala University (Collaboration)
- University of Warwick (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- UNIVERSITY OF MANCHESTER (Collaboration)
- Lund University (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- International Rice Research Institute (Collaboration)
- Rothamsted Research (Collaboration)
- University of Stellenbosch (Collaboration)
- JOHN INNES CENTRE (Collaboration)
- CRANFIELD UNIVERSITY (Collaboration)
- Swiss Institute of Bioinformatics (SIB) (Collaboration)
- UNIVERSITY OF LEEDS (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- UNIVERSITY OF ESSEX (Collaboration)
- University of Stirling (Collaboration)
- Institute Of Cardiometabolism And Nutrition (Collaboration)
- University College London (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- Lancaster University (Collaboration)
- Newcastle University (Collaboration)
- University of Bristol (Collaboration)
- Oxford Nanopore Technologies (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- University of Sussex (Collaboration)
- ETH Zurich (Collaboration)
- University of Huddersfield (Collaboration)
- ABERYSTWYTH UNIVERSITY (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- National Institute of Agronomy and Botany (NIAB) (Collaboration)
- University of Antwerp (Collaboration)
- UNIVERSITY OF DUNDEE (Collaboration)
- KING'S COLLEGE LONDON (Collaboration)
Publications
Aase-Remedios ME
(2022)
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle.
in BMC genomics
Abdul-Aziz AM
(2019)
Acute myeloid leukemia induces protumoral p16INK4a-driven senescence in the bone marrow microenvironment.
in Blood
Afouda B
(2018)
Genome-wide transcriptomics analysis of genes regulated by GATA4, 5 and 6 during cardiomyogenesis in Xenopus laevis
in Data in Brief
Al-Jourani O
(2023)
Identification of d-arabinan-degrading enzymes in mycobacteria
in Nature Communications
An SQ
(2020)
An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR.
in BMC microbiology
Andreani NA
(2020)
A reasonable correlation between cloacal and cecal microbiomes in broiler chickens.
in Poultry science
Armstrong C
(2018)
Genomic associations with bill length and disease reveal drift and selection across island bird populations
in Evolution Letters
Avramova MM
(2023)
Global Effects of the Developmental Regulator BldB in Streptomyces venezuelae.
in Journal of bacteriology
Batista MB
(2018)
Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae.
in Nucleic acids research
Bawn M
(2020)
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.
in PLoS genetics
| Description | This award provides scalable infrastructure for high-throughput DNA analysis of biological systems from ecosystems to individual cells. Embedded in the Earlham Institute's data intensive research environment and backed by one of the largest high-performance computing systems dedicated to bioscience in Europe, the National Capability in Genomics and Single-Cell Analysis is uniquely positioned to deliver the tools, resources, and services needed to tackle global issues through genome science. Genomics is transforming our understanding of biology at an accelerating pace. Open, cost-effective access to the latest technologies under the expert guidance of highly-trained staff is essential to translating advances in the field into innovation and impact for the UK bio-economy. The National Capability in Genomics and Single-Cell Analysis supports research in plants, microbes, and animals, with a particular focus in agriculture science and bioscience for health. It also plays a key role in bio-monitoring by providing rapid genomic analysis of plant pathogens during outbreaks, such as ash dieback. The newly established single-cell analysis facility extends the remit of the national capability from organisms to individual cells, providing new insights into cellular diversity within living systems at a resolution not possible before. |
| Exploitation Route | This award provides essential infrastructure and expertise for bioscience, including tools, facilities, and services available to the wider community for research and development across academia and industry. |
| Sectors | Agriculture Food and Drink Environment Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | Emerging technologies for food security. The award provided the technology, data, and expertise that underpinned the development of new biological resources for the sustainable production of improved crop varieties (wheat) and aquaculture strains (tilapia). Covid-19 response. The expertise and infrastructure supported by this award made a strong contribution to the Earlham Institute's response to Covid-19, quickly mobilising its resources to assist initial efforts to expand testing capacity locally and deploying mass testing for the benefit of local and regional communities. |
| First Year Of Impact | 2020 |
| Sector | Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal Policy & public services |
| Description | Meeting with Sir John Kingman to discuss UKRI strategy and the sustainability of Institutes |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Description | Membership of BBSRC Transformative technology Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline |
| Description | NERC 'Omics Review. I provided advice on the Environmental omics strategy as a memeber of the NERC Environmental omics steering committee |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The report generated has led to the NERC commissioning of an environmental omics facility to improve the delivery of the NERC strategy and to train the next generation of scientists. |
| URL | http://environmentalomics.org/steering-committee-and-editors/ |
| Description | NERC Deep Dive Working Group on Scientific Support and Facilities |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | 17ALERT Mid-range equipment initiative - Ultra High-Throughput Sequencing for Norwich Research Park and the UK National Capability in Genomics |
| Amount | £767,827 (GBP) |
| Funding ID | BB/R014329/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 10/2018 |
| Description | BBSRC NRPDTP Studentship - Can there be only one? Exploring heterogeneity in RNA splicing at single-cell resolution. |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2022 |
| Description | BBSRC National Bioscience Research Infrastructure: Transformative Genomics |
| Amount | £588,637 (GBP) |
| Funding ID | BBS/E/ER/23NB0006 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2028 |
| Description | Defining mechani1sms of CD8+ T-cell mediated immunity - using an integrated longitudinal model to achieve an elusive goal. |
| Amount | £532,434 (GBP) |
| Funding ID | BB/S017151/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 07/2024 |
| Description | Defining mechanisms of CD8+ T-cell mediated immunity - using an integrated longitudinal model to achieve an elusive goal. |
| Amount | £321,908 (GBP) |
| Funding ID | BB/S017178/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2020 |
| End | 01/2024 |
| Description | Developing a low-cost marker discovery platform to unlock the breeding potential of orphan crops |
| Amount | £10,000 (GBP) |
| Organisation | Knowledge Transfer Network |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 08/2020 |
| Description | Development of single-cell sequencing technology for microbial populations |
| Amount | £149,610 (GBP) |
| Funding ID | BB/R022526/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 06/2019 |
| Description | FTMA4 - Earlham Institute Flexible Talent Mobility Account |
| Amount | £107,000 (GBP) |
| Funding ID | BB/X017761/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | Feasibility study investigating circulating peripheral mitochondrial DNA as a potential non-invasive biomarker for diagnosis and surveillance of high risk cutaneous melanoma |
| Amount | £97,677 (GBP) |
| Funding ID | EDDPMA-May21\100026 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2022 |
| End | 02/2024 |
| Description | Follow On Fund - Utilising Illumina sequencing for high throughput genotyping of wheat |
| Amount | £147,471 (GBP) |
| Funding ID | BB/P004857/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2017 |
| End | 06/2018 |
| Description | Follow On Fund Pathfinder - CropQuant - Next-generation cost-effective crop monitoring system for breeding, crop research and digital agriculture |
| Amount | £10,936 (GBP) |
| Funding ID | BB/P028160/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 08/2017 |
| Description | IPA Industrial Partnering Award - Resistance: DNA methylation and the evolution of pesticide-resistance genes in aphids |
| Amount | £289,489 (GBP) |
| Funding ID | BB/R009481/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | NRP Seed fund |
| Amount | £16,000 (GBP) |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 01/2019 |
| Description | NRP Seed fund - A collaboration between the Earlham Institute (EI) and the University of East Anglia (UEA) to understand the role of small RNAs in complex gene regulatory networks in bread wheat |
| Amount | £15,000 (GBP) |
| Funding ID | SLSF 68 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 01/2019 |
| Description | NRP Seed fund - Deconstructing somites using advanced genomics approaches |
| Amount | £7,000 (GBP) |
| Funding ID | SLSF 66 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2018 |
| Description | New Investigator Award: Developing single-cell isoform sequencing tools to explore the diversity and regulation of alternative splicing in haematopoiesis |
| Amount | £726,658 (GBP) |
| Funding ID | BB/P022073/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 10/2020 |
| Description | Open plant fund - Single cell pollen meiosis screening in wheat |
| Amount | £4,000 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 07/2018 |
| Description | Responsive Mode - Wheat Pan-Genomics |
| Amount | £1,084,628 (GBP) |
| Funding ID | BB/P010768/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 05/2020 |
| Description | SPARK award - Developing a low-cost marker discovery platform to unlock the breeding potential of orphan crops |
| Amount | £10,000 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 12/2020 |
| Description | Scientific/Clinical Research Grant - Development of a 'multi-fluor-omic platform' to functionally interrogate the calcium signalling pathway in colorectal tumours: implications for cancer prevention and chemotherapy |
| Amount | £20,124 (GBP) |
| Funding ID | 16-12R |
| Organisation | Big C Cancer Charity |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2017 |
| End | 09/2018 |
| Description | Single-cell cancer evolution in the clinic - zero rating |
| Amount | £2,024,295 (GBP) |
| Funding ID | C309/A26815 |
| Organisation | Cancer Research UK |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 10/2023 |
| Description | TSB Collaborative R&D |
| Amount | £147,902 (GBP) |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2020 |
| End | 04/2022 |
| Description | Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches |
| Amount | £300,000 (GBP) |
| Funding ID | 213731/Z/18/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 05/2023 |
| Description | Wellcome - Sir Henry Wellcome Postdoctoral Fellowship - Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches |
| Amount | £300,000 (GBP) |
| Funding ID | 213731/Z/18/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 04/2023 |
| Title | Develop a cost-effective, multi-omics single-cell platform for the community |
| Description | At EI we have developed and implemented a number of single cell approaches: 1) Smart-seq2 for single cell RNA-seq This method is currently being translated into the genomics pipelines group, to be offered as a service through NC1. It enables sequencing library preparation from single-cells sorted into 96-well plates, with a transition to 384-well plates envisioned in the coming year. Through automation and volume reduction we have introduced ~10 fold reduction in library preparation costs. 2) Single cell whole genome amplification by multiple displacement amplification We have optimised Qiagen's single cell whole genome amplifcation kit to work at 1/4 volumes, allowing whole genome amplification for approximately £4 per cell. This work has been supported by a TRDF awarded to Neil Hall and Iain Macaulay. 3) Single cell multi-omics approaches, including G&T-seq We have established G&T-seq at EI and are currently developing it further to translate it to 384 well plates, enabling further cost savings and broadening applicability to include pollen sequenencing and environmental single-cell sequencing. 4) Flourescence Activated Cell Sorting At the foundation of all of this, we have established a cell sorting capability at EI - the only one in Norwich with the capability for single-cell sorting - and have worked up protocols for gut and bone marrow stem cell isolation, bacterial sorting and sorting from environmental samples. We currently support a number of research programmes across the NRP with cell sorting. 5) 10X genomics single-cell RNA-seq We have implemented the 10x genomics single cell RNAseq protocol and have used to to develop our own research work but also to support applications emerging from NRP researchers. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | As part of the development of this platform we have been successful in obtaining the following funding: 1) BBSRC New Investigator grant (Iain Macaulay) 2) BBSRC TRDF (Neil Hall, Iain Macaulay) 3) Wellcome Trust Henry Wellcome Postdoctoral Fellowship (Edyta Wojtowicz, Iain Macaulay) 4) NRP seed award (Andrea Muensterberg, Iain Macaulay, Wilfried Haerty) 5) Open Plant pilot funding (Ashleigh Lister, Iain Macaulay) 6) NERC responsive mode (Simone Immler (UEA), Iain Macaulay) 7) BBSRC DTP studentship (Iain Macaulay) 8) CRUK Accelerator Award (Giovanni Tonon (Milan), Iain Macaulay) The capability has also enabled the submission of several other responsive mode grants with local and national collaborators. These grants enable us to scale up the single-cell activities at the institute and build a cohort of expertise to support translation of methods to pipelines. We have are involved in collaborations with researchers from Imperial College (Bangham Lab), King's London (Grubb Lab) and UCL (Enver Lab) in developing and adapting single-cell multi-omics methods (e.g. G&T-seq) to specific needs in immunology, neurobioogy and haematological malignancies, respectively. We have also been able to deliever practical training in single cell genomics, either on an ad hoc basis to lab visitors, or through a formal week-long programme delivered in December 2018. |
| Title | Development of ChIP-Seq protocols in bread wheat |
| Description | The investigation of epigenetic marks enables deeper understanding of the gene expression regulation and the annotation of non coding functional sequences. Histone modifications (methylation, acetylation) are among the epigenetic marks most commonly assayed and specific modifications can be associated with biochemical activity (transcription, repression) and genomic elements (enhancers, promoters, coding regions). The protocols for chromatin immunoprecipation and sequencing have previously been developed for the model organism Arabidopsis thaliana, but never successfully applied to complex plant genomes such as the bread wheat. The protocols aimed to 1) improve the efficiency of chromatin extraction, 2) assay the antibodies, 3) evaluate yield and suitability of different tissues (leaves, root, spikelet, internode) fresh or frozen. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The protocols will enable in depth understanding of gene expression regulation in bread wheat and relative crops. The protocols will directly be used to deliver objectives within the Designing Future Wheat (BBS/E/T/000PR9783), Signatures of Domestication and Adaptation (BBS/E/T/000PR9818), Regulatory interactions and Complex Phenotypes (BBS/E/T/000PR9819) awards. The protocols will be made available to the communities through the Supporting EI's ISPs and the UK Community with Genomics and Single Cell Analysis (BBS/E/T/000PR9816) award. |
| Title | Development of a high-throughput, automated pipeline to detect SARS-COV-2 in human samples |
| Description | We established a high-throughput, automated RNA extraction and qPCR pipeline to detect SARS-COV-2 in human swab samples. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | We used our pipeline to carry out 12,000 COVID-19 tests at the Norwich Research Park and University of East Anglia The project allowed to identify and isolate over 200 asymptomatic infections among University staff and students, helping to reduce the transmission of the virus in the local community. |
| URL | https://academic.oup.com/jpubhealth/advance-article/doi/10.1093/pubmed/fdaa194/5942928 |
| Title | High throughput single-cell library preparation |
| Description | Using the IDOT liquid handling robot to produce 1536 indexed single-cell libraries |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | Major reduction in plastic use (95%), reagent use (90%) and sequencing cost (40%) over previous approaches. |
| Title | High-throughput, sequencing-based screening of environmental single-cell eukaryotes |
| Description | We developed a high-throughput screening method to characterise environmental protists from individual cells. The method is adapted from existing approaches to separate DNA and RNA contained in individuals cells for high-throughput sequencing (G&T-seq). Using bioinformatics tools, the method allows taxonomic profiling of protist species at single-cell level. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | It is too early to assess the impact of this method. |
| Title | LITE 2.0: an improved library preparation pipeline for low-cost, high-throughput whole-genome sequencing |
| Description | Low-Input Transposable Enabled (LITE) is a low-cost, short-read library preparation workflow for high-throughput processing of DNA samples from nanogram quantities. This approach, which is particularly suited for the analysis of large cohorts and population-scale studies, is widely used by EI and the wider bioscience community. We developed LITE 2.0 as a replacement for the original LITE method, incorporating both incremental and step-change improvements. The most significant improvement stems from the use of an alternative enzyme for the DNA fragmentation step, which dramatically reduces bias in regions with high GC content. LITE 2.0 is also more reproducible and amenable to higher levels of multiplexing on patterned flowcells. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | While it is too early to assess impact, LITE 2.0 is now in use at EI and accessible to the wider bioscience community through the NBRI in Transformative Genomics. |
| Title | Low-Input, Transposon Enabled (LITE) library preparation |
| Description | Whole genome sequencing (WGS) has become a standard assay in biological research, with wide-ranging applications from agriculture and bio-manufacturing to healthcare. While the cost of sequencing has sequencing has decreased by several orders of magnitude since the release of the first human genome, library preparation techniques to prepare samples for sequencing have remained relatively expensive, making WGS for large number of samples prohibitive for all but the best funded projects. Our new method addresses this limitation by using miniaturisation and automation to deliver low cost library preparation at scale from nanograms amounts of material for the analysis of large-cohorts or population-scale studies. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | The LITE technique has been available to the wider bioscience community via the National Capability in Genomics since 2018. Since its release, the technique has been accessed by over 15 institutions in the UK to process approximately 30,000 samples across a range of species from bacteria to crops and insects. |
| Title | Method for sequencing individual microbial cells and mapping SNP to reference genome data |
| Description | We have developed a method for sequencing individual bacterial cells and happy the resulting data to reference genome data to phase SNPs and identify sub populations growing within planktonic cuture. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | This has been used to identify the impact of low concentration antibiotics on mutation rate. |
| URL | https://www.biorxiv.org/content/10.1101/2020.08.25.266213v1 |
| Title | Method to obtain high-quality, long sequencing reads from insect body parts |
| Description | We have developed laboratory methods to isolate high molecular weight DNA from body parts of small insects and generate high-quality long reads from small amount of starting material. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | The method was used to generate a high-quality genome assembly from a single bee. |
| Title | Methyl-seq methods for wheat |
| Description | Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high- quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | As yet not known |
| Title | promoter exon capture platform |
| Description | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Currently being used by DFW, CIMMYT and US CAPS projects |
| Title | 6,086 high-quality Salmonella genomes |
| Description | The dataset is the output of the 10,000 Salmonella genomes project, an international collaborative effort led by Neil Hall (Earlham Institute) and Jay Hinton (University of Liverpool). The project was funded by the RCUK Global Challenge Research Fund, to sequence invasive non-Typhoidal Salmonella from developing countries on the Development Co-operation Directorate (DAC) list of Official Development Assistance (ODA) recipients. All of the sequence data generated have been deposited in the European Nucleotide Archive under the project accession number PRJEB35182. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | Any researcher can download the data generated and compare it to other sequenced genomes. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB35182 |
| Title | Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 1: Supplementary Table 1. Assembly statistics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se... |
| Title | Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 1: Supplementary Table 1. Assembly statistics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se... |
| Title | Additional file 1 of Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding |
| Description | Additional file 1: Table S1. Summary of NDM founder varieties and sequencing coverage. Table S2. Summary of overlap in sites called from wheat breeders' genotyping array and SNP sites called in founders from sequencing data. Table S3. Summary of evidence for introgressions segregating among NDM founders. Table S4. Summary of trial inputs and conditions in 2016-17 (year 1) and 2017-18 (year 2). Table S5. Description of all phenotype measurement methods and timings. Table S6. Best Linear Unbiased Estimate for all phenotypes in 504 RILs. Table S7. Summary of all genome-wide significant QTL associations found for SNP-based and Haplotype-based mapping. Table S8. Gene-Deletion-Score (GDS) loci with GDS-phenotype associations with logP> 6. Table S9. Summary of crossing scheme. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Limited_haplotype_diversit... |
| Title | Additional file 1 of Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding |
| Description | Additional file 1: Table S1. Summary of NDM founder varieties and sequencing coverage. Table S2. Summary of overlap in sites called from wheat breeders' genotyping array and SNP sites called in founders from sequencing data. Table S3. Summary of evidence for introgressions segregating among NDM founders. Table S4. Summary of trial inputs and conditions in 2016-17 (year 1) and 2017-18 (year 2). Table S5. Description of all phenotype measurement methods and timings. Table S6. Best Linear Unbiased Estimate for all phenotypes in 504 RILs. Table S7. Summary of all genome-wide significant QTL associations found for SNP-based and Haplotype-based mapping. Table S8. Gene-Deletion-Score (GDS) loci with GDS-phenotype associations with logP> 6. Table S9. Summary of crossing scheme. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Limited_haplotype_diversit... |
| Title | Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se... |
| Title | Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se... |
| Title | Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se... |
| Title | Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se... |
| Title | Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se... |
| Title | Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se... |
| Title | Dataset for Automated Purification of DNA Origami with SPRI Beads |
| Description | |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://archive.researchdata.leeds.ac.uk/1190/ |
| Title | First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing |
| Description | Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Too early to assess impact. |
| URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.5mkkwh787 |
| Title | NIAB DIVERSE MAGIC GENOTYPES AND PHENOTYPES |
| Description | SNP Genotype and Phenotype datasets for the NIAB DIVERSE MAGIC wheat population and its founders. The diverse MAGIC wheat population was developed at the National Institute for Applied Botany (NIAB), from whom germplasm is available (contact James Cockram).Summary of the Data Sets available here:(i) Founder_Consensus_Genotypes.calls.adjusted.txt, All_MAGIC_Consensus_Genotypes.calls.adjusted.txt: Tab-delimited genotypes of the 16 founders of the NIAB DIVERSE MAGIC wheat population and for 550 MAGIC lines, obtained using the 35k Wheat Breeders' Array. Calls were made using the Axiom Best Practices Genotyping Analysis workflow with an inbreeding penalty of 4. The released genotypes have consensus calls where multiple samples were genotyped from the same line. In addition, the genotypes at sites with no minor homozygous calls have been adjusted.(ii) FOUNDERS.tar, MAGIC_PLINK.tar: Genotypes in PLINK format of 1.1M imputed SNPs from exome capture in the 16 founders and and low -coverage sequencing in 505 MAGIC lines.(iii) MAGIC_PLINK_PRUNED.tar 55k tagging SNP genotypes of 505 MAGIC lines, suitable for GWAS(iv) MAGIC_PHENOTYPES.txt Phenotypes for the MAGIC lines and founders.(v) BASIC_GWAS.tar contains the genotypes and phenotypes and analysis scripts packaged into one file. We provide a simple pipeline for genetic mapping with these data.Once unpacked, the 'DATA' subdirectory contains the phenotypic data and the tagging set of ~55k SNP sites called in 504 inbred lines. In this directory, we include R functions for association mapping (file mixed.model.functions.r), including a mixed model transformation to remove the inflationary effects of unequal relatedness on genetic associations. Association mapping can be run on the basis of SNPs or the inferred founder haplotype dosages. To run, follow the steps in the R script example.analysis.r (this will run without modification if the downloaded directory is used as the R working directory). We also include a function for plotting the results as a manhattan plot (plot.functions.r). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Too early to asses impact. |
| URL | https://rdr.ucl.ac.uk/articles/dataset/NIAB_DIVERSE_MAGIC_GENOTYPES_AND_PHENOTYPES/14388461 |
| Title | PRJEB31845 - Comparison of 3L and 3DL in wheat |
| Description | Comparison of 3L and 3DL in wheat |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Comparison of 3L and 3DL in wheat has led to a publication in Biorxiv; doi: https://doi.org/10.1101/571133 |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB31845 |
| Title | PRJEB32354 - Small RNA transcriptomics comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. |
| Description | Small RNA transcriptomics comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset has resulted in a peer reviewed publication |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB32354 |
| Title | PRJEB32366 - RNA-seq comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. |
| Description | RNA-seq comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset has resulted in a peer-reviewed publication |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB32366 |
| Title | PRJEB33767 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB33767 |
| Title | PRJEB33948 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34003 - Red clover Trifolium pratense high-quality genome |
| Description | Red clover Trifolium pratense high-quality genome assembly USING OUR PIPELINE DEVELOPED IN WP1 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Used as the reference for a new dataset for a GCRF funded project. |
| Title | PRJEB34119 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34119 |
| Title | PRJEB34120 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34120 |
| Title | PRJEB34121 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34121 |
| Title | PRJEB34122 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34122 |
| Title | PRJEB34123 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34123 |
| Title | PRJEB34124 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34124 |
| Title | PRJEB34125 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34125 |
| Title | PRJEB34126 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34126 |
| Title | PRJEB34127 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34127 |
| Title | PRJEB34131 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34131 |
| Title | PRJEB34357 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34358 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34359 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34373 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34375 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34385 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34386 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34387 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34388 -Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34594 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34594 |
| Title | PRJEB34595 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34595 |
| Title | PRJEB34596 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34596 |
| Title | PRJEB34597 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34597 |
| Title | PRJEB34598 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34598 |
| Title | PRJEB34599 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34599 |
| Title | PRJEB35182 - 10k Salmonella Project |
| Description | 10k Salmonella Project sequencing - A worldwide effort to understand the epidemiology, transmission and virulence of invasive non-Typhoidal Salmonellosis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset has resulted in one publication. The data has been made public so it will form a genomic resource for the Salmonella community. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB35182 |
| Title | PRJEB35461 - Secale cereale L. inbred line 'Lo7' genome assembly |
| Description | Thie database contains the Illumina RNA-Seq and the PacBio Sequel reads for the submission of the Secale cereale L. inbred line 'Lo7' genome assembly paper |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset has resulted in a bioRxiv pre-print publication. This is a key KWS rye line so will be used in their rye breeding programme. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB35461 |
| Title | PRJEB35709 - Sequencing and assembly of 5 wheat lines |
| Description | Sequencing and assembly of Claire, Paragon, Robigus, Cadenza and Weebil hexaploid wheat lines |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Contribute to understanding of wheat lines. Part of an international collaboration with 10+ wheat genome project. Data being used by UK wheat breeders and researchers across the UK. Uploaded into EMSEML plants. http://www.10wheatgenomes.com/ |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB35709 |
| Title | PRJEB36511 - Tilapia genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36512 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36513 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36631 - 612 Vietnamese Rice Genomes |
| Description | Sequencing of 612 Vietnamese Rice Genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Contribute to understanding of Vietnamese Rice Genomes |
| Title | PRJEB37024 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | PRJEB37025 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | PRJEB37026 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | Paneth cell, stem cell - Salmonella infection transcriptomics data |
| Description | We orally infected mice with GFP-tagged Salmonella, and then isolated small intestinal crypts, containing Paneth cells and stem cells. We also did the same for uninfected (control) mice. Follwoing the cell isolation, we sorted the cells for those that were GFP positive (contained Salmonella). Then we generated a transcriptomics profile of Paneth cells directly infected with Salmonella; stem cells directly infected with Salmonella; Paneth cells not directly infected with Salmonella but cells from the infected mice; stem cells not directly infected with Salmonella but cells from the infected mice as well as Paneth cells and stem cells from the control mice. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The data now enables us to identify transcriptomics changes in host cells directly or indirectly infected by Salmonella. Also, we can now test Salmonella mutants and compare those gene expression profiles with this wild-type Salmonella induced changes. |
| Title | Single cell RNA sequencing of HSC, MkP, CFU-E including the lineage information recovered as RNA barcodes |
| Description | This dataset contains single cell RNA sequencing of blood stem cells, megakaryocytic progenitors, erythroid progenitors from control and platelet-depleted animals. Also lineage information-RNA barcodes are included in this dataset. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | This dataset enabled me to submit the manuscript, which is under revision. Furthermore, it allowed me to develop new collaborations with scientists from Australian National University and Cambridge University. |
| Title | Supporting data for "A Galaxy-based training resource for single-cell RNA-seq quality control and analyses" |
| Description | It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and the later analysis.
We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a 'visualise-filter-visualise' paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data. We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | Swiss Institute of Bioinformatics (SIB) |
| Country | Switzerland |
| Sector | Charity/Non Profit |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | University of Antwerp |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | University of Iceland |
| Country | Iceland |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | A high-quality reference genome for Arctic charr |
| Organisation | Uppsala University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | This collaboration forms part of the ERGA Pilot Project, established, funded, and driven entirely by a pan-European consortium of multidisciplinary scientists dedicated to generating a high-quality, complete genome for all European species. We used our expertise and infrastructure in biodiversity genomics to assemble and annotate a high-quality, annotated reference genome for the Arctic charr, a highly-adaptable fish species reared for aquaculture and an important part of the sustenance economy in Arctic and Subarctic communities. |
| Collaborator Contribution | Collaborators at the University of Iceland acted as Sample Ambassador for Arctic charr in the ERGA Pilot Project, identifying and providing the focal individual for genome assembly, contributed comparative data, and participated in the data analysis. Collaborators at the University of Antwerp generated HiC data for phasing and scaffolding. Collaborators at Wellcome Trust Sanger Institute curated the final assembly. Collaborators at Uppsala University evaluated the assembly using population genomics data. Collaborators at Uppsala University The ERGA Pilot Project is highly multi-disciplinary in nature, bringing together field biologists, ecologist, taxonomists, technical specialists and data scientists to build high-quality reference genome for biological specimens. |
| Impact | Khrystyna Kurta, Mats Pettersson, Arianna Cocco, Han Xiao, Sigurður S. Snorrason, Arnar Pálsson, Zophonías O. Jónsson, Karim Gharbi, Mariano Olivera Fedi, Kjetil Hindar, Linda Laikre, Nils Ryman and Leif Andersson. First Insights into Genetic Differentiation among Sympatric Morphs of Arctic Charr based on Whole-Genome Sequencing. 7th International Symposium on Genomics in Aquaculture (GIA2024). |
| Start Year | 2021 |
| Description | Bangham Lab - Imperial College London |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Working with the Bangham Lab we have been developing customised single-cell multi-omics approaches to enable parallel analysis of cell transcriptomes and viral integration sites in the genome. We have hosted visits from post-docs from Prof. Charles Bangham's lab to develop these methods. |
| Collaborator Contribution | Prof. Charles Bangham's group has expertise in the isolation and analysis of T-cells from patients with viral infection (HTLV, HIV), they have isolated cells by FACS and worked with us at EI to modify our G&T-seq protocols to enable us to link viral integration sites with changes in gene expression. |
| Impact | Several lab visits |
| Start Year | 2017 |
| Description | Cell sorting to explore metabolic stress in blood stem cells |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have provided training and expert advice in terms of cell sorting and genomics |
| Collaborator Contribution | They have generated samples from experimental models to allow testing of (for example) mitochondrial transfer between different blood cell progenitors |
| Impact | ROS-mediated PI3K activation drives mitochondrial transfer from stromal cells to hematopoietic stem cells in response to infection. Mistry JJ, Marlein CR, Moore JA, Hellmich C, Wojtowicz EE, Smith JGW, Macaulay I, Sun Y, Morfakis A, Patterson A, Horton RH, Divekar D, Morris CJ, Haestier A, Di Palma F, Beraza N, Bowles KM, Rushworth SA. Proc Natl Acad Sci U S A. 2019 Dec 3;116(49):24610-24619. doi: 10.1073/pnas.1913278116. Epub 2019 Nov 14. |
| Start Year | 2017 |
| Description | Collaborative UEA and Earlham Institute Drosophila dementia model |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Access to expertise and equipment. |
| Collaborator Contribution | Provision of materials, intellectual input, and expertise. |
| Impact | Pilot data to support further funding. |
| Start Year | 2019 |
| Description | Cytiva - Single-cell transcriptomes |
| Organisation | Cytiva |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Data comparing the new device with other methods available on the market. EI performed single-cell transcriptomic analysis using EI's 10X Genomics Chromium platform and Illumina NovaSeq 6000 system, followed by detailed bioinformatic analysis and generated data. |
| Collaborator Contribution | Cytiva have developed a new device for the disaggregation of human and animal solid tissue and tumors into viable single cells. |
| Impact | New product application note |
| Start Year | 2020 |
| Description | Dual RNA-seq collaboration with University of Lancaster (Dr Alexandre Benedetto) |
| Organisation | Lancaster University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Implementation of new laboratory protocol, provision of reagents, supervisory time, and technical expertise; 5 day accommodation and travel costs for Dr Alejandra Zarate-Potes. |
| Collaborator Contribution | Secondment of Alejandra Zarate-Potes for a week and in-kind contribution preparing and shipping C. elegans-bacterium samples |
| Impact | No published outputs yet. Alejandra Zarate-Potes secured a £7000 Joe Welsh scholarship from Lancaster University to support the development of dual RNAseq approaches in C. elegans with the Earlham Institute sequencing facility. |
| Start Year | 2021 |
| Description | ENQ-1027 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genomic data generation to underpin programs in genome adaptation. |
| Collaborator Contribution | Provision of materials |
| Impact | Chracterisation of the genomics of adaptation to climate in a stored product pest |
| Start Year | 2017 |
| Description | ENQ-1349 |
| Organisation | Lund University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | Genome data generation to assess mutations in barley genomes. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of the molecular process in plants related to design of plant architecture, time to flowering, chlorophyll biosynthesis and wax biosynthesis |
| Start Year | 2018 |
| Description | ENQ-1643 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in biodiversity and metabarcoding |
| Collaborator Contribution | Provision of materials |
| Impact | Metabarcoding data to further understanding of biodiversity environments |
| Start Year | 2017 |
| Description | ENQ-1965 |
| Organisation | University of Warwick |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptome data generation to underpin research into structure and functioning of rhizosphere in communities of oilseed rape. |
| Collaborator Contribution | Provision of materials |
| Impact | Understanding of function of root associated microbiota and root responses to it. |
| Start Year | 2017 |
| Description | ENQ-1969 |
| Organisation | University of Huddersfield |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in archaeogenetic research |
| Collaborator Contribution | Provision of materials |
| Impact | Archaeogenetic information from mitochondrial genome sequence to track human movement. |
| Start Year | 2017 |
| Description | ENQ-2007 |
| Organisation | University of Dundee |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data to create a reference transcript dataset of arabidopsis. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources to better understand plant response. |
| Start Year | 2019 |
| Description | ENQ-2007 |
| Organisation | University of Dundee |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptome data generation to underpin programs in Arabidopsis gene response |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptome data of bredth of tissues and conditions for Arabidopsis to enable a reference transcript dataset to be generated. |
| Start Year | 2017 |
| Description | ENQ-2214 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in sustainable agriculture |
| Collaborator Contribution | Provision of materials |
| Impact | A better understanding of the genetic mechanism responsible for variation in vernalization response in Brassica. |
| Start Year | 2017 |
| Description | ENQ-2279 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to generate genome reference sequences. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand and characterise plant leaf and flower growth. |
| Start Year | 2017 |
| Description | ENQ-2331 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in sustainable agriculture |
| Collaborator Contribution | Provision of materials |
| Impact | Better understanding of variation in polyploid wheat |
| Start Year | 2017 |
| Description | ENQ-2331 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in sustainable agriculture |
| Collaborator Contribution | Provision of materials |
| Impact | Better understanding of variation in polyploid wheat |
| Start Year | 2017 |
| Description | ENQ-2467 |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in food health and disease. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise a large collection of clostridium botulinum samples |
| Start Year | 2018 |
| Description | ENQ-2530 |
| Organisation | Canterbury Christ Church University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transriptome data generation to underpin programs in plant genetics |
| Collaborator Contribution | Provision of materials |
| Impact | Understanding the epigenetics of alternative splicing in Arabidopsis |
| Start Year | 2017 |
| Description | ENQ-2656 |
| Organisation | University of Sussex |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in adaptation. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of adaptation in fish genomes. |
| Start Year | 2017 |
| Description | ENQ-2656 |
| Organisation | University of Sussex |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in adaptation. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of adaptation in fish genomes. |
| Start Year | 2018 |
| Description | ENQ-2675 |
| Organisation | Institute Of Cardiometabolism And Nutrition |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Genome data generation to underpin programs in human microbiome research. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of impact of nutrition on microbiome |
| Start Year | 2017 |
| Description | ENQ-2791 |
| Organisation | Cranfield University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptome data generation to underpin programs in plant genetics. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptome data for Solanum tuberosum to enable a differential expression study. |
| Start Year | 2018 |
| Description | ENQ-2903 |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to assess variation in rice and chickpea genomes. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in crop species. |
| Start Year | 2018 |
| Description | ENQ-2962 |
| Organisation | University of Dundee |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptome data generation to assess cold response in Arabidopsis |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of the cold-response of Arabidopsis. |
| Start Year | 2018 |
| Description | ENQ-2998 |
| Organisation | University of Exeter |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in guppy evolution. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to undestand genetic diversity and evolution in guppies. |
| Start Year | 2018 |
| Description | ENQ-3218 |
| Organisation | University of Bristol |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin research into agricultural parasites. |
| Collaborator Contribution | Provision of materials |
| Impact | Genome data to improve genetic resources for isolates of Trypanosoma parasites. |
| Start Year | 2018 |
| Description | ENQ-3225 |
| Organisation | Aberystwyth University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transriptome data generation to underpin programs in plant-microbe interactions. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of the response of Brachypodium to pathogens. |
| Start Year | 2018 |
| Description | ENQ-3235 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in human reproductive genetics. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of allele frequency in human sperm cells |
| Start Year | 2018 |
| Description | ENQ-3355 |
| Organisation | Newcastle University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in environmental microbiome research. |
| Collaborator Contribution | Provision of materials |
| Impact | Further understanding of microbiome diversity. |
| Start Year | 2018 |
| Description | ENQ-3476 |
| Organisation | National Institute of Agronomy and Botany (NIAB) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to assess genetic variation in wheat lines. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in crop species. |
| Start Year | 2019 |
| Description | ENQ-3521 |
| Organisation | Rothamsted Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in fungal genetics. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to support research into the wheat pathogen Zymoseptoria tritici. |
| Start Year | 2019 |
| Description | ENQ-3538 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data to assess gene expression differences in primula. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources to better understand plant response. |
| Start Year | 2019 |
| Description | ENQ-3544 |
| Organisation | Institute Of Cardiometabolism And Nutrition |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Metagenomic data to assess human microbiome from faecal samples. |
| Collaborator Contribution | Provision of materials. |
| Impact | Genomic resources to better understand microbiome content. |
| Start Year | 2019 |
| Description | ENQ-3556 |
| Organisation | University of Exeter |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in aphid research. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise a large number of aphid clones. |
| Start Year | 2019 |
| Description | ENQ-3608 |
| Organisation | University of Exeter |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data to assess gene expression in aphids. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources to better understand gene expression in aphid. |
| Start Year | 2019 |
| Description | ENQ-3628 |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation to underpin programs in parasite biology. |
| Collaborator Contribution | Provision of materials |
| Impact | Characterisation of the genomes of parasite organisms. |
| Start Year | 2019 |
| Description | ENQ-3713 |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | Genome data generation to assess genetic variation in wheat lines. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in crop species. |
| Start Year | 2019 |
| Description | ENQ-3740 |
| Organisation | Rothamsted Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data to assess gene expression in wheat and arabidopsis. |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources to better understand plant response. |
| Start Year | 2020 |
| Description | ENQ-3859 |
| Organisation | International Rice Research Institute |
| Country | Philippines |
| Sector | Charity/Non Profit |
| PI Contribution | Genome data generation of rice samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in rice genomes. |
| Start Year | 2021 |
| Description | ENQ-3917 |
| Organisation | ETH Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Genome data generation of a cattle sample |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in cattle genomes. |
| Start Year | 2020 |
| Description | ENQ-3957 |
| Organisation | University of Oslo |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data to assess smoltification process in atlantic salmon. |
| Collaborator Contribution | Provision of materials. |
| Impact | Transcriptomic resources to better understand the smoltification process. |
| Start Year | 2019 |
| Description | ENQ-3982 |
| Organisation | University of Stellenbosch |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Genome data generation of human samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand human genomics. |
| Start Year | 2021 |
| Description | ENQ-4041 |
| Organisation | University of Manchester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Metagenomic data generation of bacterial and fungal communities in the rhizosphere |
| Collaborator Contribution | Provision of materials |
| Impact | Metagenomic resources to characterise the functional genome in bacterial and fungal communities in the rhizosphere |
| Start Year | 2020 |
| Description | ENQ-4072 |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of trypanosome samples |
| Collaborator Contribution | Provision of materials |
| Impact | Resources to better understand trypanosome genomes. |
| Start Year | 2021 |
| Description | ENQ-4137 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of human samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in human samples |
| Start Year | 2020 |
| Description | ENQ-4309 |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data generation for annotation of chicken and pig genomes |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for annotating chicken and pig genomes |
| Start Year | 2021 |
| Description | ENQ-4355 |
| Organisation | Imperial College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Transcriptomic data generation of fungal pathogens causing disease in amphibians |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources to understand variation in different lineages of a fungal pathogen. |
| Start Year | 2020 |
| Description | ENQ-4467 |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Transcriptomic data generation for benchmarking |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for benchmarking. |
| Start Year | 2020 |
| Description | ENQ-4506 |
| Organisation | University of Stirling |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of Cotton bollworm population samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to study understand population genomics of Cotton bollworm. |
| Start Year | 2021 |
| Description | ENQ-4664 |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of common buckwheat samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to better understand variation in common buckwheat. |
| Start Year | 2021 |
| Description | ENQ-4738 |
| Organisation | University of Stirling |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Trancriptomic data generation of salmon samples |
| Collaborator Contribution | Provision of materials |
| Impact | Transcriptomic resources for understanding biological variation and response in salmon. |
| Start Year | 2021 |
| Description | ENQ-4907 |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of zebrafish samples |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand variation in zebrafish |
| Start Year | 2021 |
| Description | ENQ-5006 |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Genome data generation of pea samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resources to characterise and understand pea varieties |
| Start Year | 2021 |
| Description | ENQ-5092 |
| Organisation | University of Essex |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Metabarcoding data generation of environmental samples. |
| Collaborator Contribution | Provision of materials |
| Impact | Genomic resource to classify and characterise microbial communities |
| Start Year | 2022 |
| Description | Genome annotation of five rodent genomes |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generated genome annotations for Acomys cahirinus, Acomys kempi, Acomys percivali, Acomys russatus and Onychomys torridus. |
| Collaborator Contribution | Provided material for RNA-Seq |
| Impact | Manuscript in preparation |
| Start Year | 2018 |
| Description | Genome annotation of wheat |
| Organisation | Helmholtz Zentrum München |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Integrated alternative gene models for nine wheat accessions |
| Collaborator Contribution | Generated alternative gene models for nine wheat accessions |
| Impact | ongoing |
| Start Year | 2018 |
| Description | Grubb Lab - King's College London |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have an established collaboration wiith the Grubb lab at KCL, who research neuronal plasticity. Our group has provided support in development of customised single cell multi-omics approaches to enable processing of manually picked, patch clamped single cells. |
| Collaborator Contribution | The Grubb lab have expertise in the isolation and analysis of single neurons. |
| Impact | Poster presentation at Sinagpore single cell meeting: Single-cell transcriptomics of experience-dependent neuronal plasticity Marcela Lipovsek1, Lorcan Browne1, Darren Byrne1, Eilis Hannon2, James Lipscombe3, Iain Macaulay3, Jonathan Mill2, Matthew Grubb1 |
| Start Year | 2017 |
| Description | Impact of low protein diet on liver function upon Salmonella infection |
| Organisation | Quadram Institute Bioscience |
| Department | Gut Health and Food Safety |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My team has performed FACS cell sorting and 10X analysis of immune cells in the liver. |
| Collaborator Contribution | Dr Beraza holds the project license enabling studies of the Salmonella infection and impact on liver function in M. musculus. Her team provided the expertise in immune cell isolation from the liver. |
| Impact | We are writing the manuscript, running title: Low protein diet exerts protective effect on liver function upon Salmonella infection. |
| Start Year | 2021 |
| Description | Mead Lab - Oxford - Long Read Sequencing of Single Cells |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We advised on long-read sequencing of single-cell libraries, performed library prep and organised sequencing. |
| Collaborator Contribution | They prepared samples and cDNA, designed the experiment/ |
| Impact | Data generation at EI. |
| Start Year | 2019 |
| Description | No Amp Targeted Enrichment with University of Cambridge (Dr Sebastian Eves-van den Akker) |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Implementation of new lab protocol and data generation |
| Collaborator Contribution | Provision of material, data analysis |
| Impact | No published output yet. |
| Start Year | 2020 |
| Description | Panhematopoietic clonal and molecular analysis using RNA-barcoding approach |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I was performing FACS sorting of cells, isolated samples were included in published papers. |
| Collaborator Contribution | Dr Rushworth and his team provided wild type (C57Bl6, n=25) and PEPC Boy (n=20) mice and skills (intravenous injections). |
| Impact | Publications: 10.1172/JCI153157 10.1101/2022.05.16.491933 10.3389/fimmu.2022.1003006 10.1073/pnas.1913278116 10.1182/bloodadvances.2022007033 |
| Start Year | 2019 |
| Description | Phased resistance gene enrichment sequencing ( |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Access to equipment and expertise. |
| Collaborator Contribution | Provision of material, intellectual input, and expertise. |
| Impact | New tools to characterise and exploit disease resistance genes in wheat. |
| Start Year | 2019 |
| Description | Single-cell DNA/RNA analysis of zebrafish sperm |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | we provide training, expertise and infrastructure for single-cell sequencing |
| Collaborator Contribution | UEA lead Simone Immler provides experimental design, samples and project leadership |
| Impact | Grant - https://gtr.ukri.org/projects?ref=NE%2FS011188%2F1 |
| Start Year | 2018 |
| Description | Single-cell RNA analysis of Arabidopsis protoplasts |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | we provide expertise and support in the generation and analysis of single-cell rna-seq libraries from tapetal protoplasts |
| Collaborator Contribution | Xiao Feng's group provide samples, biological focus and analysis |
| Impact | manuscript in preparation, three presentations at EI's single-cell symposium |
| Start Year | 2016 |
| Description | Sub-cellular biopsy RNA-analysis (Paolo Actis/Lucy Stead, University of Leeds) |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have provided advice and training in single-cell and low input RNA seq to a postdoc from Lucy Stead's lab in Leeds |
| Collaborator Contribution | They have visited our labs to work with us on developing ultra-low input RNA-seq approaches |
| Impact | Development of ultra-low input RNA-seq approach. Training of staff from Leeds in single-cell RNA-seq. |
| Start Year | 2019 |
| Description | Understanding the immune cell profile driving elevated breast cancer progression following antibiotic-induced microbiota disturbances |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Access to equipment and expertise. |
| Collaborator Contribution | Provision of material, intellectual input, expertise. |
| Impact | PhD student trained in single-cell analysis. |
| Start Year | 2019 |
| Description | Understanding the immune cell profile driving elevated breast cancer progression following antibiotic-induced microbiota disturbances |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Access to equipment and expertise. |
| Collaborator Contribution | Provision of material, intellectual input, expertise. |
| Impact | PhD student trained in single-cell analysis. |
| Start Year | 2019 |
| Title | EIMAP - alignment qc pipeline |
| Description | Eimap maps reads to a suitable reference genome yielding additional insight into the quality of sequencing data and identifying bad quality samples not detectable by raw data QC. EIMAP determines metrics such as alignment rate and insert size, for RNA-seq, additional metrics include ribosomal RNA content and reference-guided transcriptome assemblies. Results are reported in an interactive HTML report. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | The pipeline is run for all EI illumina sequencing runs, helping ensure delivery of high quality sequencing data. |
| Title | Large scale bacterial assembly and annotation with the bgrr| pipeline |
| Description | The bacterial genome reconstruction and recognition pipeline (bgrr|), is an open-sourced, customizable pipeline management system for large-scale bacterial genomics providing de novo assembly and annotation. The pipeline is designed to facilitate the efficient processing of large batches of bacterial/microbial samples (e.g. as obtained from EI LITE-libraries) and has been designed to deal with samples of varying size and quality. bgrr| is written in Python3 and orchestrates a full bioinformatics workflow including library quality assessment, read preprocessing, de novo assembly and annotation using well-established third party software tied together with several Snakemake pipelines |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Impact | Our large-scale bacterial assembly and annotation pipeline (Bgrr|) originally developed to support EI's involvement in the 10K Salmonella project (a collaboration with the University of Liverpool), the pipeline has now been successfully applied to a number of external projects. |
| Title | Mikado - Leveraging multiple transcriptome assembly methods for improved gene structure annotation |
| Description | Mikado is a lightweight Python3 pipeline to identify the most useful or "best" set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Mikado has been utilised to deliver improved gene annotation for Ash doi:10.1038/nature20786 and wheat doi: 10.1101/gr.217117.116 and was utilised by the international wheat genome sequencing consortium. |
| Title | Portcullis - Efficient and accurate detection of splice junctions from RNAseq |
| Description | Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions. Both the filtered junctions and BAM files are cleaner and more usable resources which can more effectively be used to assist in downstream analyses such as gene prediction and genome annotation. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Porcullis has been utilised to deliver improved gene annotation for Ash doi:10.1038/nature20786 and wheat doi: 10.1101/gr.217117.116 and was utilised by the international wheat genome sequencing consortium. |
| Title | REAT - Robust and Extendable eukaryotic Annotation Toolkit |
| Description | REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Being used to support EI's annotation projects including the DToL Protist project Components of the toolkit were developed to support the annotation of wheat accessions as part of the 10+ Wheat Genome Project. |
| URL | https://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core |
| Title | Smart-Seq2 quality control pipeline |
| Description | Smart-seq2 quantification and quality control pipeline, developed for single-cell service at the Earlham Institue. Starting with the FASTQ files generated from the SmartSeq2 experiment and a sample sheet containing the appropriate metadata, transcript level counts are generated, merged and used to produce QC metrics. A QC report document is generated for each of the plates, and the whole experiment. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Used as a standard part of Earlham single cell QC |
| Title | ei-annotation - eukaryotic annotation pipeline |
| Description | Eukaryotic genome annotation pipeline |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Annotation pipeline being utilised to support http://www.10wheatgenomes.com/10-wheat-genomes-project-and-the-wheat-initiative/ |
| Title | minos - a gene model consolidation pipeline for genome annotation projects |
| Description | Minos is a Python3/Snakemake - based pipeline that generates and utilises metrics derived from protein, transcript and expression data sets to consolidate gene models obtained from gene annotation workflows. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | The tool has bee used to deliver annotation for 9 wheat accessions as part of the 10+ Wheat Genomes Project (http://www.10wheatgenomes.com/) and is being used to support a variety of Earlham Institute annotation projects |
| URL | http://www.10wheatgenomes.com/ |
| Description | 10 years of impact: keeping living things healthy |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article about impact at EI. From Salmonella to ash dieback: ten years of impact on how we understand human health and that of the environment. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/10-years-impact-keeping-living-things-healthy |
| Description | 2022 Wellcome Trust Biomedical Vacation Research Scholarships and UKRI-BBSRC Norwich Research Park Biosciences Doctoral Training Partnership Summer Scholarships |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | The undergraduate student from the University of Galway, Ireland had the opportunity to work on the project: " Identifying molecular drivers influencing the impact of low protein diet on hematopoietic cells in the bone marrow niche" for 8 weeks. The student had the opportunity to acquire skills of data handling and analysis using relevant R packages, present data and participate in a series of workshops on career development in STEM. The student got familiarized with cell culture and flow cytometry. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Activity - Where have you BEEn? |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Activity at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Year(s) Of Engagement Activity | 2019 |
| Description | Article - Why is genome annotation important? |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Article EI website - Why is genome annotation important? Highlighting annotation tool developed and training activities |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/why-genome-annotation-important |
| Description | BBC News, Darwin Tree of Life |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Professor Neil Hal, Dr Iain Macaulay and Dr Karim Gharbi were interviewed by the BBC following the funding of announcement of the Darwin Tree of Life Project by the Wellcome Trust. The interview emphasised the role of the Earlham Institute in the project and showcased the expertise and equipment of the National Capability in Genomics and Single-Cell Analysis. The interview was initially broadcast nationally on the one o'clock news and later broadcast internationally on BBC World. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.youtube.com/watch?v=itTQhO7XKiY |
| Description | BBC Radio Norfolk Interview on Norfolk Day |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Karim Gharbi was interviewed with by BBC Radio Norfolk host Stephen Bumfrey on the 27th of July, 2019 to celebrate Norfolk Day and Norwich Research Park. The interview was pre-recorded from the Earlham Institute's sequencing labs and focused on the cutting-edge technologies used by the Institute and their impact on people's lives. The interview was interactive and involved the radio host navigating the wheat genome using online tools to look at gluten genes, followed by a discussion on gluten intolerance in the human population and associated genetic risks. The interview was recorded in the morning and broadcasted in the afternoon. The recording was also made available on the BBC website for download for 90 days post broadcast. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.bbc.co.uk/programmes/p06bth9z |
| Description | Bread and butter: decoding wheat - 12/08/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article outlining the key contributions from the Earlham Institute in the sequencing, assembly, annotation and analysis of the wheat genome including work led through the CSP. This article highlights the coordinated and integrated efforts led through EIs CSP, DFW and research grants to improve our knowledge and understanding of this economically critical crop. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/bread-and-butter-decoding-wheat |
| Description | Conference talk: Tackling microbial diseases using MinION diagnostics and NanoOK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited plenary speaker at the Bern Nanopore Technology Day. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Contribution to online science teaching platform |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | Dr Karim Gharbi was interviewed by Developing Experts, a Norwich-based company, providing a growing library of over 700 interactive online science lessons with fun science experiments, handouts and assessment for learning activities for children 4 to 14 years. The platform is used by 4,000 home educators and teachers in the UK and abroad. The interview was carried out in situ within the National Capability laboratories in the form short films, which are featured in lessons about DNA, inheritance, and genetics. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://developingexperts.com/articles/168 |
| Description | Day in the life of a genome unscrambler and paperback lover |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article by Monica Della Rossa, Research Assistant in the Genomics Pipelines Group speaking about how her DNA curiosity led to working in next generation sequencing. Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/day-life-genome-unscrambler-paperback-lover |
| Description | Digital oral presentation at 14th congress of European Crohn's and colitis organisation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference oral presentation at the 14th congress of European Crohn's and colitis organisation. Presentation tited "the regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches". Digital oral presentation at main congress and also an oral presentation at the Y-ECCO basic science workshop. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ecco-ibd.eu/ecco19.html |
| Description | EI Innovate 17 November 2022 (In-Person) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | In its fourth year, EI Innovate is an annual engagement event that explores opportunities for innovation and collaboration among attendees from agri-food, biotech and med-tech sectors. The theme of EI Innovate 2022 was 'tackling urgent global challenges through pioneering research' and served to highlight specific areas where EI's research is generating impact, driven by a targeted programme delivered by Group Leaders, members of faculty and departmental heads. This year was held purely in an in-person format, and on a single day to maximise accessibility for attendees. Three key themes were represented across the programme of talks: Food Security and Environment Sustainability (the impact of genomes on crop breeding, and improving aquaculture with genomic resources for tilapia breeding); Enabling others to advance research and innovate (advancing and enabling data-intensive bioscience, and sharing expertise through training); and Improving Human Health (Genomic approaches to understand the emergence of virulence and AMR in Salmonella, and preventative lifestyle modifications). A registration fee of £50 covered refreshments and lunch for delegates. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2022#programme |
| Description | EI Innovate 17-18 November 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | In its third year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was delivered as an online-only format, spread across two days, with each half-day session focusing on one of the three themes: 1) Natural products & biomanufacturing - exploring how synthetic biology and data-driven approaches can facilitate the discovery of new bioactive compounds and develop biomanufacturing platforms based on plants 2) AI in plant science - exploring how AI and ML tools and techniques can help with the understanding of many biological functions in plants that underline important economic traits such as resistance to pathogens, nutrient utilisation and structural development 3) Omics approaches to study the human gut microbiome - exploring how bioinformatics, systems biology and machine learning approaches can be used for advanced microbiome analysis and to facilitate personalised microbiome treatments, identification of novel biomarkers and pathogens, and antimicrobial resistant features of our microbiota. Sharing examples of existing collaborations, this event was a chance to explore new opportunities. The two sessions on day 1 were structured with three talks, one from EI faculty and two from external collaborators, a Q&A panel discussion, and group networking on Spatial. The second session on AI also included flash talks from the Alan Turing Institute Fellows. The third session on the morning of day 2 took the format of several short talks from groups leaders and PhD students, followed by a Q&A panel discussion and further networking opportunities in spatial in the afternoon. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-innovate-2021-linking-datasets-and-bioscience |
| Description | EI Innovate 17-19 November 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | In its second year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was converted to an online only format, spread across three days, with each day focussing on one of the three themes: 1) Disease identification and monitoring - how genomics and bioinformatics are used for disease identification and monitoring, from COVID-19, to AMR to agricultural pathogens. 2) Finding a needle in a haystack - Identifying specific targets in health and disease with long read RNA and single cell sequencing. 3) Accelerating plant breeding with next generation genetics, genomics and epigenetics. Sharing examples of existing collaborations, this event was a chance to explore new opportunities. Each day was structured with two talks, one from EI faculty and one from an external collaborator, a Q&A panel discussion, facilitated break out discussions and then slots to arrange one-to-one meetings with other participants in the afternoon (event times 09:30-15:30), arranged using the software Meeting Mojo. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/ei-innovate-2020 |
| Description | EI Innovate: 13 November 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate: genomics data to advance bioscience, held on 13th November 2019, was a success. It was attended by 82 people, 26 EI staff who delivered talks, tours and discussion sessions, prepared posters and came to network, 31 representatives from industry (across agri-food, biotech and life sciences sectors), 2 BBSRC staff, 2 representatives from Food Standards Agency, representatives from KTN, NALEP, National Biofilms Centre and Centre for Process Innovation, and 14 representatives from (9 from UEA) academic institutions. We attracted 3 high profile external speakers from: Natural History Museum (Director of Research); Royal Botanic Gardens Kew (Director of Science); and Oxford Nanopore Technologies (Vice President for Applications). We delivered 5 talks, prepared 11 posters, led 2 tours of Genomics Pipelines and Bio-Foundry to showcase EI expertise and capabilities. The afternoon programme had 3 breakout sessions, aiming to explore opportunities for collaborative projects: 1. New Frontiers in Next-Generation Sequencing 2. Data Mining of the UK Tree of Life to Understand and Utilise Biodiversity of British Species 3. A guided discussion about the value of data for driving research, innovation and commercialisation This was EI's first externally-facing KEC event, bringing together various stakeholders to learn about EI expertise and how it can add value to their projects. We received a lot of informal positive feedback and following upon the interactions that this event enabled. A date has already been secured for November 2020. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/innovate2019-0 |
| Description | EI Long Read RNA Symposium 15-17 June 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this inaugural symposium focusing on Long Read RNA technologies and applications, we combined use cases of long read RNAseq, sample processing hints and tips from experts in sequencing facilities at Earlham Institute and SciLifeLab National Genomics Infrastructure, plus technology developments from leading long read technology companies with break out groups to discuss particular challenges faced in use of long read technology for: Genome Annotation; Differential Expression (gene and transcript) and Networks; and Sample processing and Low input single cell applications. We accepted abstract submissions, which were all offered as lightning talks, encouraging PhD students and ECRs to present their research. The majority of attendees were PostDoctoral researchers (52%), with significant attendance from PhD and Postgraduate students (35%) and 10% PI/group leaders, with the remainder identifying as undergraduate or 'Other' categories, demonstrating the relevance of this event to those at varying stages of their career due to the rapid development of this technology. Furthermore, 59% of attendees were from the UK, with the remainder spread across a further 9 countries, expanding the reach of EI's expertise. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-long-read-rna-symposium-2021 |
| Description | EI Socioeconomic impact report 2022 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to publicise a socioeconomic impact report undertaken on the Institute's research. In forecasting future impact, the report was designed to demonstrate the quality and breadth of our work to our funders, stakeholders, and the wider public. Figures from the report have since been used in presentations and at other events. Feedback has been positive and demonstrates an increased awareness of EI impact and the areas of research we're engaged in. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-economic-impact |
| Description | EI boost National Capability in Genomics and Single Cell Analysis with ultra-high throughput sequencing platform |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release to announce that Earlham Institute (EI) add Illumina's NovaSeq 6000 to its National Capability in Genomics and Single Cell Analysis, harnessing the power of ultra-high throughput sequencing for Norwich Research Park and the wider bioscience community. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/ei-boost-national-capability-genomics-and-single-cell-analysis-ult... |
| Description | Earlham Institute becomes signatory to the Technician Commitment |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of ongoing work in developing equality, diversity and inclusive culture at EI, the article shares news of our joining the Technician Commitment initiative. The aim of the piece was to raise awareness of our joining of the initiative, communicate this pledge to our staff and students, and highlight our next steps with the wider scientific community. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-becomes-signatory-technician-commitment |
| Description | Earlham Institute's Flexible Talent Mobility Account Award, 3 day bespok workshop at Earlham Institute |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Supported by Earlham Institute's Flexible Talent Mobility Account Award (BB/W510890/1) we hosted a visitor (JJW) from University of Southampton for a 3 day workshop for myself and one other participant (MB). Skills: 1.obtaining stable droplet with beads 2. obtaining droplets with a megakaryocyte and a bead 3. generating libraries from emulsion Skills developed during the workshop with Dr. West will help me facilitate my own research. Through discussions and ad hoc troubleshooting, I have gained more confidence in setting up the microfluidic device. I have realised which further improvements I can implement to further optimise the current set up. After implementing them I will perform library construction of captured cells. Importantly, we have obtained high rate of 1 in 7 cells being conecapsulated with the bead. Through discussion with Dr West we can further increase it applying Dean entrainment system to reach coencapsulation rate of 1 in 2 cells. After implementing these modifications, I will pursue library construction using generated emulsion. This was an extension of a previus workshop (February 2022), which facilitated the generation of preliminary data for new funding options including: 1. Joint application for a PhD student funded or co-funded by British Heart Foundation 2. BBSRC standard research grant I intend to apply for Wellcome Career Development Award (call September 2022) including preliminary data generated during this workshop. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Emma's Antarctic Diary - 15/04/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website blog article highlighting the work of Emma Langan, a PhD student in EI's Leggett group who has been on a six-week expedition to Antarctica to analyse the effects of climate change on coccolithophores with real-time DNA sequencing algorithms. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media and showcase the work of our staff. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/emma-langan-antarctic-adventure-algae-climate-change |
| Description | Excellent science? It's in the technical detail |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on the Institute's status as a Technician Commitment signatory, designed to inform and influence the opinions of internal and external audiences. We saw a positive response internally as people felt recognised and saw visibility given to colleagues who may have been overlooked for their past contributions. The piece also invited ideas for follow-up content on the different kinds of technical roles and their contributions. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/excellent-science-its-technical-detail |
| Description | Exotic Wheat DNA news story |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News story to highlight new publication from an EI researcher, with the aim of generating media coverage to engage with industry, professional practitioners, and the general public. National, local, and trade media covered the story, which saw an increase in visitors to the website, strong engagement on social media, and queries directed at the authors. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/exotic-wheat-dna-could-help-breed-climate-proof-crops |
| Description | FTMA4, visit at MRC Stem cell institute, Cambridge |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDRA< RA and a group leader visited the lab at MRC Stem Cell Institute to gain practical knowledge and experience in new cell assays. Possibility of joint funding application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Festival of Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a talk entitled "Defining Cell Identity with Single-Cell Omics" - about 50+ people were in the audience, which was a broad "genomics" audience including PhD students, postdocs etc. Some good discussions with researchers afterwards. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.festivalofgenomics.com/home |
| Description | Flexible Talent Mobility Account Launch Workshop - 21 March 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | This workshop brought together ten (10) industry representatives from seven (7) different companies, ranging from Information Technology/Hardware, to transnational consumer goods companies, breeders and Research and Development companies with some of our project leaders to discuss potential areas for collaboration and skills transfer. We have since awarded seed funding to initiate pilot projects engaging EI faculty with companies in attendance for this workshop. In addition a number of NDAs are under development. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/flexible-talent-mobility-account-and-workshop |
| Description | Flow Cytometry Workshop 26 February 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training was a one-day lecture/theory-based workshop aimed at those who have access to Flow Cytometers and were in the planning stages of a project which would require their use. The two trainers were external experts - Dr Rachael Walker, running the Babraham Institute facility; Dr Derek Davies, running the facility and training/outreach associated at the Crick Institute. Aimed at beginners in the early planning stages of their experiments, the 21 attendees comprised mainly PhD students (~38%) and PostDocs (~28.5%) with other facility/service providers also in attendance. Feedback is still be collected and reviewed at the time of reporting. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/flow-cytometry-training |
| Description | Focus on the future at EI Innovate |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Write-up of the EI Innovate event held at the Earlham Institute in November 2022, designed to provide an overview of the topics discussed to those who were unable to attend or may want to follow up with speakers having been here. The piece received some positive engagement and comments on social and will be a valuable tool for encouraging registration for the 2023 event. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/focus-future-ei-innovate |
| Description | Genome Annotation Workshop 13-15 April 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this first iteration of the Genome Annotation workshop, we delivered a series of conceptual/theory lectures with hands-on sessions, allowing delegates to practice using software to reinforce learning, all hosted within specially created virtual machines (hosted on Cyverse-UK). Sessions covered: an overview of relevant sequencing technologies; benefits of different platforms to inform experimental design; characteristics of a good quality sample and likely to produce viable sequencing data; how to assess quality of RNAseq data; de novo and reference-guided transcriptome assembly including processing long read data; alternative approaches for annotating protein coding genes in eukaryotes; hands-on experience with tools and pipelines developed at EI (Mikado and Portcullis). Attendees were predominantly from the UK (65%) with the remainder from overseas including Australia and the USA, with 60% being Postdoctoral researchers, ~20% PhD students and the remainder PIs/group leaders and 'Other'. All attendees were from academia. Delegates rated the course overall as 'Very good' or 'Excellent' (92%), and trainers as knowledgeable ('Very good' or 'Excellent' 100%) and 100% would recommend the course. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/genome-annotation-workshop-2021 |
| Description | Genome Annotation Workshop 2022 17-19 May (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This 3-day course, our second iteration of this workshop, provided scientists with an overview of eukaryotic genome annotation approaches, covering advances in Next Generation Sequencing (NGS) technologies, transcriptome assembly, and best practice guidance for building gene models utilising short and long read sequencing data or cross species proteins. It also covered how to integrate and assess different gene models and create a publication/release ready gene set. These topics were delivered via a series of conceptual/theory lectures with hands-on sessions, all hosted within specially created virtual machines (hosted on Cyverse-UK). Attendees were predominantly PhD students (40%), or professional practitioners including bioinformaticians, assistant professors and research scientists. The remainder were post-docs, Professors/PIs and lecturers. 100% would recommend the course. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/genome-annotation-workshop-2022 |
| Description | Genome Science - Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk on single-cell isoform sequencing at Genome Science Conference. Gave opportunity to highlight the work we are doing on the BBSRC New Investigator Grant. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://genomescience.co.uk/programme/ |
| Description | Genome Technologies and Innovation Workshop - 31 October 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organised in conjunction with UEA, having attracted funding from Research England, this workshop and symposium attracted 58 people from across the Norwich Research Park, including a number of small companies (e.g. Tropic Biosciences and Food Forensics), plus larger, multi-national companies involved in genome and related technologies. It showcased the wide-ranging expertise of researchers across the park as well as the facilties and equipment, plus announcing winners of a pilot project award, funded jointly by 10X Genomics and Illumina to access the institute's facilities. The final session of the workshop was a closed session exploring potential engagement with both small and large enterprises with genomics and related technologies. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/genome-technologies-and-innovation-workshop |
| Description | ITV News, Darwin Tree of Life |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Professor Neil Hal, Dr Iain Macaulay and Dr Karim Gharbi were interviewed by the BBC following the funding of announcement of the Darwin Tree of Life Project by the Wellcome Trust. The interview emphasised the role of the Earlham Institute in the project and showcased the expertise and equipment of the National Capability in Genomics and Single-Cell Analysis. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.itv.com/news/anglia/2019-11-08/cambridge-scientists-to-help-map-genomes-of-all-life-on-b... |
| Description | Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress |
| Year(s) Of Engagement Activity | 2019 |
| Description | Immersive Visit Training Program (LM_18) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Genomics Pipelines Group hosted a scientist from the Biosciences eastern and central Africa - International Livestock Research Institute (BecA - ILRI) Hub for 1 week. The purpose of the visit was to be introduce to scientist to the latest advances in NGS sequencing platforms (primarily Illumina) from library preparation to platform operation and management, and share best practices. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Inside EI - 21/05/2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Inside EI is an open day when the public are invited to learn more about the work at the Earlham Institute, meet our team and engage with our research and understand its relevance and impact. There were talks and posters based on CSP-led research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://earlhaminstitute.coveragebook.com/b/0ee62ba7 |
| Description | Inside EI - Open Day 2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | One day in May 2019 EI opened its doors to the public and schools from the region. Offering an overview of the Tree of Life with the branches of our tree culminating in posters displaying colourful imagery of our research, visitors were able to talk to researchers about their projects and why the research is important. There were hands on activities providing insight into de novo genome assembly, nanopore sequencing technology, synthetic biology and high performance/cloud computing. In addition to the activities, there were talks and tours of the laboratories, which were fully subscribed. We were joined by schools from across the region in the morning, and opened our doors to the general public for the afternoon, with a total of over 400 visitors, media coverage (TV and radio) reaching an estimated 500+. The feedback was incredibly positive and we achieved an unbelievably successful set of outcomes. Comparison of pre- and post Open Day attitudes demonstrated that: Participants reported very high increases in understanding of a range of topics, while overwhelmingly agreed that research at EI should be funded by the government. The majority of people left with an increased appreciation of the importance of bioinformatics, genomics, etc. for their every day life, the environment, and more. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact |
| Description | Inside EI: Public engagement with impact - 06/08/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website highlighting the Inside EI event for the public to explore our fascinating and diverse range of important scientific research projects including talks and posters on our CSP work and the importance and impact of public engagement in research |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact |
| Description | Inside Earlham Institute: purchasing snazzy kit for the Genomics Pipelines lab |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article Harbans Marway, Research Assistant in the Genomics Pipelines Group, explaining why quality control is key in Genomics Pipelines, and the right equipment makes life easier in a next-generation genome sequencing lab. Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/inside-earlham-institute-purchasing-snazzy-kit-genomics-pipelines-... |
| Description | Internactional Society for Experimental Hematology, 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Poster presentation : 'Parallel clonal and molecular profiling of hematopoietic stem cells using RNA barcoding', initiated questions from other researchers in the field to apply this method. For now only level of discussions. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Key tilapia genome offers boost to global food security |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to highlight a new publication from EI researchers on reference genome for a key aquaculture species, designed to reach breeders, industry, and academics working in this space. Positive trade media coverage, as well as promotion from project collaborators, helped this news to reach a wide audience and enhance EI's reputation. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/key-tilapia-genome-offers-boost-global-food-security |
| Description | LITE-ing the way to game-changing technology |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on the impact of work undertaken at the Institute to reduce sequencing costs. The piece celebrates the impact these new protocols have achieved, and which we hope others will adopt where appropriate - raising awareness of the protocol among professionals and the Institute's impact on practice |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/lite-ing-way-game-changing-technology |
| Description | Lego DNA Sequencing - Blocksford Brickopore |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Iain Macaulay and Dr Richard Legget build a LEGO DNA sequencer using LEGO Mindstorms, which was displayed for use at the EI stand at the Norwich Science Festival. The instrument allowed users to "build" a 22-mer sequencer of DNA from 4 different coloured "bases" and then sequence them. Assistants from EI were then able to assist with blasting sequences and telling users what species their sequence aligned to. It was well received and we will use it agin at other outreach opportunities. The instrument even has its own twitter account (@brickopore) |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://twitter.com/@brickopore |
| Description | Linkage is a drag - 15/04/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Website article on the data-driven approached used to identify and understand more about genes that control genome-wide gene conversion or the high level of gene conversion in wheat. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. The article has estimated coverage views of 34.3K. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/linkage-drag-first-wheat-gene-rapidly-convert-defective-traits-new |
| Description | Meiosis and Beyond - 5-6 March 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | A mini symposium bringing together researchers from a wide variety of fields united by one common theme - meiosis (before, during and after). Delegates and presenters working on a variety of organisms from plants to birds to nematodes came together to hear some of the latest research using new and emerging technologies and approaches in the field of meiosis. Beyond the mini symposium the group gathered for discussions including challenges they face in common with one another, technology that could help to answer their biological questions and to roadmap where they were as a research cohort. The group are working on a paper summarising the current state and challenges and a subset have taken discussions from the workshop to successfully apply for funding to support new and emerging ideas. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/meiosis-and-beyond |
| Description | Member of MinION Analysis and Reference Consortium (MARC) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | MARC is a consortium of scientists who seek to work together to understand how to get the best out of nanopore technology and to collaborate on international experiments and publications. So far, we have published two papers together which seek to describe and evaluate MinION technology. We are now working on a third publication based on an experiment to sequence river water around the world using nanopore sequencing. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018 |
| Description | Metagenomics: Data Analysis and Interpretation 16-19 September 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Attended by approximately equal numbers of PhD students to PostDoctoral and Academic researchers (combined), this course provided an overview of metagenomic data analysis, including ample time spent on hands-on activities using example data sets and relevant tools and resources, taking delegates through to production of publication-ready figures. As a newly redeveloped course with new teaching staff, this course still received positive feedback with over 75% recommendation of the course and 70% rating trainers as Very Good or Excellent. There are some lessons learned and the training team are reviewing the course programme and structure, including leadership of the course by an individual research group to address the areas for improvement. Attendees were predominantly from the UK, with some from Europe and one from South America. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/metagenomics-data-analysis-and-interpretation |
| Description | Museum collections reveal century of growing stress on bees |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News story to publicise paper on insights gained from sequencing museum collections, with the aim of raising awareness of the plight of pollinators, influencing policy makers, and engaging audiences in the science of genomics. The story was a joint release with collaborators and generated interest on social media and some coverage, while also strengthening relationships between partners involved. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/museum-collections-reveal-century-growing-stress-bees |
| Description | New DNA on the block: Genomics expert to lead our pioneering sequencing |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News story announcing that Dr Karim Gharbi joined the Earlham Institute as Head of Genomics Pipelines to lead our UK National Capability in Genomics. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/new-dna-block-genomics-expert-lead-our-pioneering-sequencing |
| Description | New approaches for metagenome assembly with short reads |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release about newly-published novel algorithms for metagenomic assembly |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/new-approaches-metagenome-assembly-short-reads |
| Description | Norwich Pint of Science, 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation: "How rock-solid bone makes blood and heals wounds?", approximately 50 members of the general public attended an eveninng in the Maddermarket pub. Informal setting sparked questions about the production of blood cells during development, how gravitation affects stem cells and how can we manufacture these cells more efficiently. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Norwich Science Festival - The Human Mosaic |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | I gave a talk at the Norwich Science Festival to approximately 20 members of the public in which I discussed cells and how we can read genetic information from individual cells using single-cell genomics |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://norwichsciencefestival.co.uk/events/engineering-technology-day-gallery-stage/ |
| Description | Norwich Single Cell Symposium 14-16 September 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Single-cell technologies are continuing to develop rapidly and expanding in applications in the life sciences sector - in this virtual symposium we focused on the "next generation" of tools to study living systems at cellular resolution, including: Long-read/Isoform sequencing; Multi-omic analysis; Proteomics; Spatial transcriptomics. Year on year, our annual symposium has been a great platform for discussion between researchers in diverse fields (microbial, plant, biomedical) focusing on the applications of new technologies. We accepted abstract submissions for lightning talks, encouraging PhD students and ECRs to present their research. This was in place of an online poster session, which we have observed and received feedback from researchers attending other events that these are typically poorly attended. We opted for a nominal registration fee in order to minimise no shows (£15) and we observed a 90% turn-out rate. This is in comparison to the 60% turn-out observed for the free-to-attend mini symposium in 2020. In addition, the attendees, who would typically predominantly be from Norwich Research Park for face-to-face events, were again seen to come from a much wider geographic range with 30% from Norwich Research Park, 50% from other parts of the UK and the remaining ~20% International, spreading awareness of EI and our Single Cell expertise. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/single-cell-symposium-2021 |
| Description | Norwich Single Cell Symposium 16 September 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In place of our annual single-cell symposium we opted to develop a new programme of speakers for a virtual mini-symposium, hosted via Zoom, to keep our community engaged. Single-cell technologies are now widely used but continue to develop rapidly - in this mini-symposium we focussed on the "next generation" of tools to study living systems at cellular resolution, including: Long-read/Isoform sequencing; Multi-omic analysis; Proteomics; Spatial transcriptomics. Year on year, our annual symposium has been a great platform for discussion between researchers in diverse fields (microbial, plant, biomedical) focussing on the applications of new technologies. We made this event free to register in order to ascertain the interest in the community and to monitor attendance rates. We were delighted with 244 registrations and, despite the free registration we observed a 60% turn-out rate. This is in comparison to the typical 70-80 attendees we have for the face-to-face version of this symposium. In addition, the attendees, who would typically predominantly be from Norwich Research Park for face-to-face events, were from a much wider geographic range with 25% from Norwich Research Park, one-third National and almost 45% International (from 25 countries outside of the UK), spreading awareness of EI and our Single Cell expertise. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/virtual-single-cell-symposium-future-single-cell-analysis |
| Description | Norwich Single Cell Symposium 16-17 May 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The symposium was predominantly aimed at researchers across the region and attracted some 77 people with international speakers plus sponsors to discuss the latest development and challenges in the field. Offering sponsorship opportunities meant additional support for costs for the symposium but also a high degree of engagement from these sponsor companies, who were interested in our applications of Single Cell Technologies. |
| Year(s) Of Engagement Activity | 2017,2018 |
| URL | http://www.earlham.ac.uk/norwich-single-cell-symposium-2018 |
| Description | Norwich Single Cell Symposium 16-17 October 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | With approximately 70 attendees, the third Norwich Single-Cell Symposium featured speakers covering topics as diverse and neuronal development, embryonic reprogramming in humans, tapetal development in plants and splicing variation in hematopoietic stem cells, as well as a keynote lecture from Professor Sir Mel Greaves working in cancer. Delegates and sponsors enjoyed the variety of topics and opportunities for engagement through the lunch time exhibition, poster and networking sessions. Attendees were predominantly Postdoctoral researchers and industry representatives (including attendees who did not sponsor), with several group leaders and PhD students also in attendance. The training team collected live feedback using a powerpoint-based software, which proved useful in determining overall opinions (over half of the attendees provided feedback using their mobile devices). This feedback indicated a desire to repeat the symposium in 12 months, with approximately 90% of respondents in agreement with the length of the symposium, plus an overall rating of of keynote speaker and invited speakers as 4.7 and 4.5 out of 5.0, respectively, plus networking with delegates and engaging with sponsors as 4.2 and 3.9, respectively. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/single-cell-symposium-2019 |
| Description | Norwich Single Cell Symposium, 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation, "Clonal heterogeneity in anucleate cells unravelled using RNA barcoding". I have received questions regarding applicationa of the method in other systems. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Norwich Single-Cell Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Laura Mincarelli gave a talk entitled "Combined short and long read single-cell sequencing identify aging related transcriptional profile and splicing landscape in hematopoietic stem cells and progenitors" at the Norwich Single Cell Symposium (16th-17th October, 2019) |
| Year(s) Of Engagement Activity | 2019 |
| Description | Norwich Single-Cell Symposium - 8 May 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | With the developments in single-cell genomics technologies, particularly in the broadening of applications, we organised this symposium to bring together researchers who were curious about single-cell genomics with external speakers engaged in advanced single-cell research as well as highlighting the single-cell capabilities available at Earlham Institute. The idea was that this would provide an informal platform to catalyse future development and application of single-cell genomics across the region. The one-day symposium covered single-cell genomics topics in the following areas: technology development, developmental biology, health and disease, plant science and data analysis. The inaugural event had over 90 registrations, including a small number of industry representatives who had the option to sponsor and exhibit at the meeting. Feedback received suggested that the symposium offered a great diversity of topics in an informal and friendly setting. Many respondents providing feedback commented upon the high standard of presentations and enjoyable networking opportunities citing that they would like to see a repeat symposium the following year and that the meeting should be a little longer, with more networking. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/norwich-single-cell-symposium |
| Description | Nuffield Research Experience Placements Summer 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | With a continued reduction in the number of Nuffield REPs placements due to the COVID-19 pandemic and the need to move these placements online, Earlham Institute were pleased to be able to host 2 students, through a two-week research programme. Students worked in parallel, together with two of EI's PhD students, who were able to teach use of 'R' to analyse single cell data, applying their own parameters to produce different visualisations of the data, demonstrating a key point about balancing clear data with loss of data and therefore information through defining different parameters and interpreting the resulting graphs. Students were also able to research key genes of interest, identified through their analyses, and presented their work to the hosts, each other and members of the training team, demonstrating their learned skills not only in software, but also how to present and describe data for publication. |
| Year(s) Of Engagement Activity | 2021 |
| Description | ON Helix New Horizons in Genetic Screening |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | 300 participants from private sector, NHS and academia attended ON Helix workshops over 4 days to discuss progress and challenges of personalised medicine, genetic screening to open up the discussion how to tackle new challenges the field encounters. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.onhelix.com/ |
| Description | Obscure routes into science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Interview with NC1 staff member about his route into a science career |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/my-obscure-route-into-science-neil-shearer |
| Description | Old for new: using ancient genetic variation to supercharge wheat - 26/04/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A media interview and website articles on a global, collaborative effort led by the Earlham Institute, UK and CIMMYT, Mexico which sheds light on the genetic basis of biomass accumulation and efficiency in use of light, both of which are bottlenecks in yield improvement in wheat. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. This story has an estimated coverage views of 32.9K. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/old-new-using-ancient-genetic-variation-supercharge-wheat |
| Description | Oral presentation - Characterization of splicing diversity in bulk samples and single cells using long read technologies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at the Maurice Wohl Clinical Neuroscience Institute King's College London |
| Year(s) Of Engagement Activity | 2019 |
| Description | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | Pacbio UGM |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Laura Mincarelli gave a talk entitled "Integrated short and long read single cell RNA-sequencing reveals alternative splicing events in hematopoietic stem and progenitor cells" at the Pacbio User Group Meeting in Milan (November 14th 2019) |
| Year(s) Of Engagement Activity | 2019 |
| Description | PhD by experience: Darren Heavens |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article by Dr Darren Heavens, who after over 30 years' experience in genomics research, from pig breeding to improving wheat yield, went down an alternative PhD route. Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/phd-experience |
| Description | Platelet Society Early Career Researchers |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | 70 researchers including undergraduate, postgraduate students, postdocs and clinicians attended the conference to discuss advances in the field, which sparked discussions, knowledge exchange and potential new collaborations. Presentation title: "Dissecting platelet origin using novel RNA-based molecular and clonal approaches" |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation at EMBO conference Modularity of signaling proteins and networks |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster presentation titled "Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks" at the EMBO conference Modularity of signaling proteins and networks. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://meetings.embo.org/event/18-modularity |
| Description | Poster presentation at Exploring Human Host-Microbiome Interactions in Health and Disease conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster presentation titled "Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches" at the Exploring Human Host-Microbiome Interactions in Health and Disease conference 2017. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/exploring-human-host-microbiome-in... |
| Description | Poster presentation, Grodon Research Conference, March 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 200 experts around the world joined the Gordon Research Conference on Megakaryocytes and Platelets. It fostered discussions, knowledge exchange and initiated new collaborations, which otherwise would be difficult to establish. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.grc.org/cell-biology-of-megakaryocytes-and-platelets-conference/2023/ |
| Description | Poster presentation: Tackling microbial diseases of the preterm infant gut using MinION diagnostics and NanoOK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at AGBT 2018 conference, Florida, USA, February 2018. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Festival of Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | ~100 attendees at the Festival of Genomics were present for my talk on Single-cell long read sequencing |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation AGBT |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Laura Mincarelli gave a talk entitled: Integrated short and long read single cell RNA-sequencing reveals alternative splicing events in hematopoietic stem and progenitor cells at the AGBT general meeting. This was a high profile presentation in which the outputs of the new invesigator grant were first presented internationally. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation at Norwich Cancer research network |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | 20 scientists attended the presentation on new methods and their applications and how to implement them in their own research. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presentation at the Festival of Genomics and Biodata 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Presentation on RNA barcoding and its application to study the platelet biogenesis in different contexts. It sparked questions and the discussion on potential applications in other research groups and a potential interaction with the industrial partner. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://festivalofgenomics.com/london/en/page/home |
| Description | Presentation, Pint of Science, Norwich |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | I gave the presentation on the effect of diet on the immune system function. It sparked questions about the food choices impacting our immunity, health and longevity. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://pintofscience.co.uk/events/norwich |
| Description | Press release on EI Innovate 2019 event |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Press release on EI Innovate - invitation to collaborate on projects or business ideas needing our scientific expertise. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/newsroom/how-innovate-ei-applying-genomics-real-world |
| Description | Press release on Tree of Knowledge |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release about the Wellcome Trust award for the Darwin Tree of Life Project. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/earlham-institute-tree-knowledge-genomics-biota |
| Description | Press release on discovering hidden plant medicines |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release on how EI scientists are delving into the genetics of UK wildflowers to find the medicines that we never knew were right on our doorstep. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/discovering-hidden-plant-medicines-your-doorstep |
| Description | Press release: Diagnosing infections earlier in preterm babies with real time genomic analysis |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release about how scientists and clinicians at the Norwich Research Park have pioneered a new method for profiling the microbiome of preterm babies that can significantly speed-up the identification of infections and indicate more effective treatments. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/newsroom/diagnosing-infections-earlier-preterm-babies-real-time-genomic-an... |
| Description | Press release: New rapid test diagnoses pneumonia and lower respiratory infections |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release published about a new, rapid way of diagnosing bacterial lower respiratory tract infections in hours rather than days that could improve patient care and slow the spread of antimicrobial resistance. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/newsroom/new-rapid-test-diagnoses-pneumonia-and-lower-respiratory-infectio... |
| Description | Researcher visit from Rijksuniversiteit of Groningen, Groningen, Netherlands |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at EI on the history of clonal studies from bacteria to mammals, outlook into naturally occurring barcodes-possibilites and limitations. Discussion about new algorithms/pipelines to improve the analysis. Individual discussions on current practices and available pipelines. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Royal Norfolk Show 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | The EI Bee Trail was run at the Royal Norfolk Show, involving a trail activity that teaches participants about pollinators, sequencing, and food security. The idea is to inform opinions and behaviour, including providing people with a pack of wildflower seeds to plant, and to invite people to find out more about how sequencing is providing us with info that can protect biodiversity. Over two days, large school groups and families took part, reporting very positive feedback and often asking for more seeds, follow-up activities or talks. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://norwichsciencefestival.co.uk/news/science-at-the-show |
| Description | Royal Society Summer Exhibition 2022, Decoding the DNA Tree of Life |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Over 500 high school students, undergraduate, postgraduate, students, industry sponsors, academics and funders attended 5 day event at the Royal Society. It sparked conversations with high school students deciding about their future career, encouraging them start career in STEM, inspiring primary school pupils to discover new species, DNA and start the conversation about invisible molecules building our body. It enabled interactions with other researchers presenting their work and possible synergies between projects. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Salmonella - how the body fights back - 14/11/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Website article highlighting collaborative research from the University of East Anglia, supported by Earlham Institute (EI) which shows how the human body powers its emergency response to salmonella infection. Contributions from the Macaulay and Di Palma groups. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/salmonella-how-body-fights-back |
| Description | Scientific Advances in Agriculture 5 November 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Industry/Business |
| Results and Impact | An evening workshop organised as part of AgriTech week, this event dissemination was supported by AgriTech East. 29 people attended the evening including EI faculty, local farmers, agronomists and other related-businesses. The programme for the evening, included demonstrations with discussions as small group rotations covering: Genome Technologies in Agriculture; Can In-field AI/Robotics improve crop yield; How could Synthetic Biology impact Agriculture; What could Genomics do for Crop Advancement. Delegates were also given ample opportunity to see the facilities and ask many questions through the tours of: Genomic Pipelines Laboratory; DNA Foundry Laboratory; and Data Centre. Email requests were made to follow up on initial discussions from this workshop and to put EI experts in touch with other overseas researchers wishing to implement a similar framework. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/scientific-advances-agriculture |
| Description | Sequencing project to unleash the huge potential of euglenoids |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article promoting a new position paper from the Euglena network of scientists. Main aim was to raise awareness of the initiative among relevant scientific audience, and to profile EI's expertise and involvement in the project. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/sequencing-project-unleash-huge-potential-euglenoids |
| Description | Single Cell symposium in Cambridge, 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation :"Dissecting platelet origin using novel RNA-based molecular and clonal approaches". Overview of alternative strategies of lineage tracing implemented for the brain/iPSC reprogramming approaches. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Single Cell symposium in Cambridge, 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation: Parallel clonal and molecular profiling of hematopoietic stem cells using RNA barcoding |
| Year(s) Of Engagement Activity | 2022 |
| Description | Single-Cell RNAseq 1-4 November 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was redeveloped from the course delivered in 2020 focusing on bioinformatics only, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park (50%), and from academia (94%). They rated the training overall as very good or excellent (91%) and the trainers very good or excellent (91%), with 91% saying that they would recommend the course. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-training-course-2021 |
| Description | Single-Cell RNAseq 19-22 October 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was converted from a 5-day course that was previously split 3 days of lab work and 2 days of bioinformatics into a bioinformatics only course, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park, and from academia (88%). They rated the training overall as very good or excellent (100%) and the trainers very good or excellent (100%), with 100% saying that they would recommend the course. Despite the virtual nature of the course, there were plenty of opportunities to to discuss matters with both trainers and discuss with other delegates and there were many requests during our introductory delegate 'flash' presentations where individuals wished to reach out to each other for longer-term collaborations and/or to discuss new techniques/approaches that were presented. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-2020 |
| Description | Single-Cell RNAseq Data Analysis 7 - 10 November 2022 (Hybrid) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Single-Cell RNAseq workshop is now in its fourth year, although this was the first iteration to be conducted in hybrid format. It is aimed at students and early-career researchers in the early stages of a single-cell project and provides an introduction to single-cell genomics via a combination of lectures, hands-on bioinformatics sessions (using Smartseq and 10X protocols) and case studies from EIs own PhD cohort. Familiarity with Unix Shell and R was required. Registration was on an application basis, to establish the relevance/suitability of the course for each applicant in accordance with their project, experience, or studies. Access to virtual machines (via Cyverse UK) allowed students to access data and software required for the hands-on sessions, with access continuing to be provided for a short time after the course to allow optimal use for the attendees. All sessions were recorded and distributed to attendees. The hybrid format allowed international attendance, and while the majority were based in parts of the UK (53%) there were attendees from America (11%), Italy, Scandinavia, Spain and New Zealand. Of the 19 registrants, 4 were based at the Norwich Research Park. The majority opted for virtual attendance (74%). In terms of job function, the majority were Post Doctoral researchers and PhD students (58%), the remainder comprising Professors, bioinformaticians and data analysts. 100% rated the overall quality of the course as very good/excellent and all would recommend the course. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022#about-the-event |
| Description | Single-cell show-and-tell: Activity based tours of the EI single-cell labs |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | 40 staff from EI were given an interactive tour of the single-cell labs. We introduced them to the different platforms and concepts behind single-cell analysis. We hosted staff from operations, communications, business development and faculty, all staff at EI were invited. The event stimulated questions and discussion about both the biology and technology associated with single cell work. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Sphere Fluidics -Cambridge |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | PDRA, RA and Group Leader engaged with the industry-Sphere Fluidics to optimise bespoke microfluidc assays using their equipment. Obtained preliminary data for a grant application. The activities were supported by EI's FTMA4 award (BB/X017761/1) |
| Year(s) Of Engagement Activity | 2023 |
| Description | Ten years at EI blog |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog post by NC1 staff member about their experiences working at EI over ten years. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/ten-years-genome-sequencing-darren-heavens |
| Description | Ten years in genome sequencing: Darren Heavens |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article t by Dr Darren Heavens, Team Leader in the Genomics Pipelines Group, reflecting on 10 years of genome sequencing at EI and his evolving is role to support the National Capability in Genomics. Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/ten-years-genome-sequencing-darren-heavens |
| Description | The 25th Annual Meeting of the RNA Society. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The 25th Annual Meeting of the RNA Society. May 26th-31st, 2020. Poster, Integrated short and long read single cell RNA sequencing reveals alternative splicing events in hematopoietic stem and progenitor cells |
| Year(s) Of Engagement Activity | 2020 |
| Description | The art of being single: advanced single-cell sequencing technology |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article showcasing the single-cell sequencing capabilities at EI, with the intent of increasing collaboration and engagement with industry. The group has also used the article to connect with researchers based at EI who might benefit from discussing these technologies and approaches. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/advanced-single-cell-sequencing-technology |
| Description | The genetic machinery that drives biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article to explore research into a key species for aquaculture and how genomics approaches can inform breeding programmes. The article was used in helping to secure a podcast interview for one of the researchers. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/genetic-machinery-drives-biodiversity |
| Description | The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Updating the Inflammatory Bowel Disease community about the regulatory landscape and the role of autophagy in various types of intestinal cells |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://academic.oup.com/ecco-jcc/article/13/Supplement_1/S031/5300677 |
| Description | Tracking bacterial evolution in real time spots emergence of antimicrobial resistance |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article about a new publication focused on single-cell technology and expertise at the Institute. Primary objectives were to promote the paper and raise awareness of the Institute's expertise in single-cell genomics, and antimicrobial resistance. Piece received positive engagement on social media among research professionals |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/tracking-bacterial-evolution-real-time-spots-emergence-antimicrobial-... |
| Description | Training - Single-Cell RNAseq Training Course |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Training delivered as part of the Single-Cell RNAseq Training Course at EI. The audience included postdoctoral researchers and graduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 27-29 September 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the third iteration of the UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR-UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to discuss and present on how to manage biological data and use computational methods to power life science research. The 3-day programme combined a keynote lecture with presentations of use cases from researchers working at the cutting edge, plus breakout discussion groups at the end of each session. The breakout groups were intended for participants to exchange expertise and challenges with one another, in order to develop multidisciplinary solutions to complex problems together. Discussions and themes as a result of these breakout groups were then summarised by the facilitator at the end of each session. To maximise engagement across multiple disciplines we opted for a streamlined programme (no parallel sessions), and short introductory talks to support each session to encourage focus on the theme in question. Research facilitators also headed up each session to reinforce key themes, and encourage or stimulate conversation. The sessions covered: Metagenomics and Microbial Bioinformatics; Bioimaging and Artificial Intelligence; Sex and Gender Bias in Computational Disciplines; Federated Analytics/Learning; Structural Bioinformatics; Open Science and Spatial Transcriptomics. Over 130 delegates registered to attend the conference, the majority from the United Kingdom (~86%) however registrants were also based in the US and Europe, Asia, the Middle East and South Africa. Approximately half of these virtual attendees were Postdoctoral Researchers (52%) while other significant groups comprised PhD Students (19%) and Professor/PIs (11%). |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/uk-cbcb-2022#about-the-event |
| Description | USA FDA - presentation by Silvia Ogbeide |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | PhD Student Silvia Ogbeide gave an invited talk on Single-cell multiomics to the US FDA omics workshop in February 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit by Clive Lewis, MP |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Karim Gharbi, Head of the Genomics Pipelines Group, hosted Clive Lewis, MP for Norwich South, for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, govern |
| Year(s) Of Engagement Activity | 2019 |
| Description | Visit by UEA BSc/MSc Evolutionary Biology and Conservation Genetics students |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Leah Catchpole, Team Leader in the Genomics Pipelines Group, hosted a group of 20 BSc/MSc Evolutionary Biology and Conservation Genetics students from the University of East Anglia for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Visit by Wheat Yield Partnership researchers |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Chris Watkins, Team Leader in the Genomics Pipelines Group, hosted a group of 25 international Wheat Yield Partnership researchers from around the world for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Visit by members of the UEA Council |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Karim Gharbi, Head the Genomics Pipelines Group, hosted members of the UEA Council for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Visits by Chinese Delegation from Shaanxi Province |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Karim Gharbi, Head of the Genomics Pipelines Group, hosted a Chinese delegation from the Shaanxi province for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Visits by DEFRA Chief Scientific Adviser |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Dr Karim Gharbi, Head of the Genomics Pipelines Group, hosted DEFRA Chief Scientific Adviser for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Visits by delegation from the Chinese Academy of Agricultural Sciences |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Karim Gharbi, Head of the Genomics Pipelines Group, hosted a delegation from the Chinese Academy of Agricultural Sciences for a tour of the National Capability in Genomics at the Earlham Institute. Visits such as this are key to our efforts to engage with the wider community and communicate the impact of rapid technological advances in genomics on innovation, the economy and society. Since Mach 2018, more than 200 visitors from around the world, including students, academic researchers, industry professionals, government officials and politicians have visited the National Capability in Genomics Facilities. |
| Year(s) Of Engagement Activity | 2018 |
| Description | We're ten years old, leading the field in decoding complex, non-human genomes - 21/09/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article highlighting contributions of EI, including work delivered through the CSP in decoding complex, non-human genomes. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/ten-years-leading-decoding-complex-genomes |
| Description | Web Article - How our tools can help you: MIKADO - 23.05.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This article promotes Mikado is a novel algorithm that lets you integrate multiple RNA-Seq assemblies into a coherent transcript annotation. The performance of genomics RNA-Seq aligners and assemblers varies greatly across different organisms and experiments and the accuracy of the transcript reconstruction is boosted by combining multiple approaches. The open-source bioinformatics tool can remove redundancies and select the best transcript models according to user-specific metrics while solving common genetic artefacts. Lead developer Luca Venturini explains how Mikado leverages multiple transcriptome assembly methods for improved gene structure annotation. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/how-our-tools-can-help-you-mikado |
| Description | Web Article - Sex Cells: Meiosis at the centromere (of life science research) - 04.04.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Article for continued promotion of our successful Meiosis and Beyond workshop at Earlham Institute. It was clear how varied and encompassing research into meiosis really is. The story of evolution, for plants, animals, fungi and their parasites, begins with recombination - but the story doesn't stop there. What can we hope to untangle (other than chromosomes) in the future? |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/sex-cells-meiosis-centromere-life-science-research |
| Description | Web Article - What is bioinformatics? - 16.10.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it? Biology is going large. With the advent of next generation (and third generation) genome sequencing and along with it an explosion in the amount of biological data being produced daily, scientists are now playing with terabytes or even petabytes (lots and lots of zeros) of data at a time. It would take infinite infinities for a single person to analyse this digital abundance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/what-is-bioinformatics |
| Description | Web article - A celebration of science in Norwich - 27.08.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Promoting our engagement in the Noriwch Science festival beyond our region. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/celebration-science-norwich |
| Description | Web article - Decoding Living Systems: from cell to ecosystem - 28.03.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/decoding-living-systems-cell-ecosystem |
| Description | Web article - My week at Earlham Institute: more than just science - 29.08.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | This article promotes the experience of a work experience student to engage with others. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/my-week-earlham-institute-more-than-just-science |
| Description | Website Article: An accessible single-cell RNA seq bioinformatics training suite using Galaxy |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Detailed the development of a workflow and related training materials via the user-friendly Galaxy interface to support biologists with no prior experience in command line. This was used as part of the training course in Single-Cell RNAseq bioinformatics earlier in the year. The workflow remains freely accessible and demonstrates the longer-term impact through continued availability of our training materials and courses developed through NC4. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/accessible-single-cell-rna-sequencing-bioinformatics-training-usi... |
| Description | Website article on EI Alumni |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Article interviewing recent alumni of EI about their time here and their onward careers. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/ei-alumni-where-are-they-now |
| Description | Website article on single cell genomics |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article about the EI single cell symposium 2019 |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/exciting-developments-single-cell-genomics |
| Description | Website article: Biology's Dark Matter |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article about work with protists |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/biology-dark-matter-protists |
| Description | Website article: Our year in industry: setting the stage for a career in science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Website article published about "year in industry" placements. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/our-year-industry-setting-stage-career-science |
| Description | Website article: Why do a Year in Industry? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Web article outlining the experience of two year ins industry students undertaking a placement between September 2019 and August 2020. Focus on the research and transferrable skills, in particular the benefits of bioinformatics, that they were able to develop through their placements and how this is impacting the next steps in their careers. Demonstrates the supportive and engaging environment offered whilst learning valuable skills at EI. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-do-year-industry |
| Description | Website article: Women in Science: single-cell genomics part 1 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article interview with female researchers at EI about the most challenging and rewarding aspects of their careers so far, where we're at with gender equality, and what they'd share with those coming up the single-cell ladder. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/women-in-science-single-cell-genomics-part-one |
| Description | Website article: Women in Science: single-cell genomics part 2 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article including interviews with female researchers about their experiences. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/women-in-science-single-cell-genomics-part-two |
| Description | Website article: the human mosaic |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article about single cell genomic technologies |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/the-human-mosaic |
| Description | Workshop for MRes students in Genomics and Evolution |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | WOrkshop on capabilities enabled by single cell genomics, discussion of a selected scientific article. Critical assessment of the strengths and weaknesses of performed experiments. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Year in Industry 2020/21 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | The institute supported two Year in Industry students from mid-September with a stipend and whose expected end date is the end of August (11.5 months). Students started their placements virtually, undertaking a short rotation period within the first three weeks at the institute. During this time students were able to join faculty group weekly lab meetings, including an overview by the group leader to understand the groups' research interests and how they are connected, plus to listen to the individual providing their project update that week, and discuss potential projects on offer. They were also able to spend time with a Genomics Pipelines team leader going through protocols and other relevant introductory materials, plus guided discussions to review this information. Additionally they undertook various science communication tasks with the Communications team, sculpting news articles based on EI's research due for imminent publication, plus a presentation on the same subject intended for a lay audience. Once they had chosen a project the students were able to write their project proposal and refine this through further discussions with the project supervisor(s). The students are carrying out their research projects until approximately the end of June, when they will then concentrate on their project dissertation. One student is entirely focussed on bioinformatics work and the other has a combination of lab work to implement a new protocol for automation in conjunction with Genomics Pipelines whilst also carrying out the data analysis. |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2016,2018,2019 |
| URL | https://www.earlham.ac.uk/year-industry |
| Description | Year in Industry Programme 2018/19 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | The institute supported two Year in Industry students from mid-September with a stipend and whose expected end date is the end of August (11.5 months). Students undertook a short rotation period within the first three weeks at the institute, shadowing staff in the Genomics Pipelines teams to understand sample processing, including working with our Project management team to understand derivation of quotes and tracking of samples, then with laboratory staff through library construction and loading the sequencers. During this time students met with various potential project supervisors to discuss project ideas. Once they had chosen a project the students were able to write their project proposal and refine this through further discussions with the project supervisor. The students are carrying out their research project until approximately the end of June, when they will then concentrate on their project dissertation. The institute has also also hosted a third, unpaid intern, who started mid-September, but whose project placement is due to complete at the end of July. The student is undertaking a pre-defined research project, but still followed the other students on rotation to gain a good understanding of the institute's operational set up and core strategic programmes. |
| Year(s) Of Engagement Activity | 2011,2012,2013,2015,2016,2018 |
| URL | http://www.earlham.ac.uk/year-industry |