Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

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.

Organisations

Publications

10 25 50
 
Description This award has helped to establish and advance the single cell analysis platform at EI which is widely used across NRP and beyond. It also supports the genomics platform which underpinned the Earlham Institute CSP and the Designing Future wheat ISP.
Exploitation Route This is underpinning technical infrastructure and all data is underpinning ongoing research
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
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 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 05/2018 
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 10/2018 
End 09/2022
 
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 08/2019 
End 07/2022
 
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 07/2018 
End 06/2019
 
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 04/2018 
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 10/2017 
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 08/2017 
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 05/2017 
End 05/2020
 
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 09/2017 
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 10/2018 
End 10/2023
 
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 05/2019 
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 05/2019 
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 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 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 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 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 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 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-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 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 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 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 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/ 
 
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 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 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: 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 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 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 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 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 Viisit 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 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 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 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 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 
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 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 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: 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 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 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 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 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 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 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 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, government officials and politicians have visited the National Capability in Genomics Facilities.
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 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: 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 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