A Systems Approach to Understanding Methylation Programming in Oocytes and its Consequences in Development
Lead Research Organisation:
Babraham Institute
Department Name: Epigenetics
Abstract
The genetic information we receive from our parents is not only the DNA sequence of our genes. Genes are also marked in different ways in the egg and sperm from which we arise. These marks are referred to as 'epigenetic' marks, and one of the major types of epigenetic marking is a chemical tag on certain sites in the DNA called DNA methylation. DNA methylation marks are important because they can change the activity of the genes that they tag; dense DNA methylation on genes usually causes them to be shut down. In addition, DNA methylation marks can be faithfully copied on the DNA as cells divide, so that they can provide a form of memory on the gene to reflect earlier decisions about how that gene should be active. DNA methylation is a normal mechanism by which the body controls genes throughout our development and in response to changes in our environment or diet. However, because DNA methylation marks are easier to change than the underlying DNA sequence, DNA methylation patterns may also be more vulnerable to adverse environmental conditions and abnormal DNA methylation is commonly seen in diseases such as cancer.
In this research, we aim to understand the processes that control which of our genes are marked by DNA methylation in eggs and how these marks are transmitted after the egg is fertilised by the sperm. Eggs and sperm carry different patterns of DNA methylation, so parents can transmit different epigenetic information to their offspring and these could reflect environmental factors in their own history. DNA methylation undergoes particularly dramatic changes in the early embryo, and these transitions may be important for controlling how the embryo divides and the body plan is established and different tissues arise. We are particularly interested to discover whether the normal patterns of DNA methylation in the egg and early embryo are changed as a consequence of altered diet or processes involved in assisted reproduction techniques, such as superovulation. Poor diet - which might include protein deficiency in developing countries and fat-rich diets in the Western world - in mothers before or around the time of conception is known to increase the risk of developing diseases such as diabetes and cardiovascular disorders in later life. Knowing whether DNA methylation changes occur and why would help provide informed advice about nutrition and dietary supplements to women contemplating pregnancy. Assisted reproduction techniques, such as in vitro fertilisation, often involve harvesting eggs and culturing embryos during the time at which DNA methylation patterns are undergoing most rapid change and may be most susceptible. Therefore, it is important to know whether these techniques modify DNA methylation marks to be able to develop further improved fertility treatments and minimise the risk of creating epigenetic errors.
In this research, we aim to understand the processes that control which of our genes are marked by DNA methylation in eggs and how these marks are transmitted after the egg is fertilised by the sperm. Eggs and sperm carry different patterns of DNA methylation, so parents can transmit different epigenetic information to their offspring and these could reflect environmental factors in their own history. DNA methylation undergoes particularly dramatic changes in the early embryo, and these transitions may be important for controlling how the embryo divides and the body plan is established and different tissues arise. We are particularly interested to discover whether the normal patterns of DNA methylation in the egg and early embryo are changed as a consequence of altered diet or processes involved in assisted reproduction techniques, such as superovulation. Poor diet - which might include protein deficiency in developing countries and fat-rich diets in the Western world - in mothers before or around the time of conception is known to increase the risk of developing diseases such as diabetes and cardiovascular disorders in later life. Knowing whether DNA methylation changes occur and why would help provide informed advice about nutrition and dietary supplements to women contemplating pregnancy. Assisted reproduction techniques, such as in vitro fertilisation, often involve harvesting eggs and culturing embryos during the time at which DNA methylation patterns are undergoing most rapid change and may be most susceptible. Therefore, it is important to know whether these techniques modify DNA methylation marks to be able to develop further improved fertility treatments and minimise the risk of creating epigenetic errors.
Technical Summary
We aim to provide an overarching account of DNA methylation in oocytes, its consequences and vulnerabilities. The work will be conducted mostly in the mouse as the model of choice for understanding epigenetic processes in gametes and preimplantation embryos. The connections we shall explore between transcription and methylation are based on known properties of Dnmt3a and Dnmt3L - which constitute the de novo methylation complex active in oocytes and which is believed to sense histone modifications - and histone modifying factors with evidence for transcription-coupled activity. Of particular interest to us is methylation of H3K4 and H3K36, which can be modified in response to transcription. We shall use conditional knock-outs for factors of the Kdm1 and Kdm5 families, which regulate H3K4 methylation, and we shall mutate Dnmt3a so that it is no longer binds the transcription-coupled mark H3K36me3. We shall map transcription units and promoter activity and how they change during oocyte growth, and correlate this with timing of DNA methylation in specific genes. We shall ablate specific transcription factors expressed in oocytes, and investigate whether this leads to predicted changes in gene body and intragenic CpG island methylation. This will be done with conditional alleles for transcription factors with known roles in oogenesis, but we shall also identify additional transcription factors with effects during the de novo methylation phase of oocyte growth by informatics analysis of expression and transcription start site datasets. We shall use our highly sensitive DNA methylation profiling (RRBS) as an endpoint in many of these mechanistic studies. We shall use RRBS (and other techniques we might develop) to profile changes in methylation in oocytes and embryos in response to manipulations in maternal diet and superovulation. We shall also profile DNA methylation in human preimplantation embryos to identify conserved sites and properties of DNA methylation.
Planned Impact
The work proposed in this application is mostly of a fundamental nature in a model organism aimed at understanding epigenetic processes in germ cells and preimplantation embryos. It seeks to provide an overarching account of how and where DNA methylation is established in female gametes, what the consequences of this mark is for how genes are expressed in the oocyte and how gene activity is regulated in the early embryo. Correct epigenetic programming in gametes and embryos has a lifelong impact on development and health, because some epigenetic marks once established or lost cannot be corrected at later times in development. Although the work will be carried out mostly in a genetically tractable and informative model organism, we shall also conduct comparative analysis in human preimplantation embryos to demonstrate whether insights gained in the model organism are relevant to human embryogenesis. As well as providing fundamental knowledge, we expect that the research could help identify risks in assisted reproduction methods, enhance knowledge in stem cell research, and identify whether epigenetic marks can be destabilised by poor maternal nutrition and could directly contribute to adverse health outcomes in later life. Therefore, the knowledge acquired from this research will likely to have major impacts in fundamental epigenetics and germ cell biology research, but also potential translational impacts in human nutrition, assisted reproduction and stem cell research.
We also expect an impact of our research in the technical advances we shall continue to make in developing methods for epigenetic profiling in small numbers of cells. Such advances could have widespread application in biomedical research. We have already been approached by several groups (from both academic and pharmaceutical sectors) from research areas unrelated to our field with an interest in applying our methods to their own biomedical questions. Therefore, we anticipate significant impact in training and knowledge exchange also at a technical level.
We also expect an impact of our research in the technical advances we shall continue to make in developing methods for epigenetic profiling in small numbers of cells. Such advances could have widespread application in biomedical research. We have already been approached by several groups (from both academic and pharmaceutical sectors) from research areas unrelated to our field with an interest in applying our methods to their own biomedical questions. Therefore, we anticipate significant impact in training and knowledge exchange also at a technical level.
Organisations
- Babraham Institute (Lead Research Organisation)
- Cancer Research UK Cambridge Institute (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Technical University of Dresden (Collaboration)
- Bellvitge Biomedical Research Institute (Collaboration)
- Clermont Université (Collaboration)
- The University of Texas at San Antonio (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- UNIVERSITY OF BRITISH COLUMBIA (Collaboration)
- Vrije Universiteit Brussel (Collaboration)
- University of East Anglia (Collaboration)
- Helmholtz Zentrum München (Collaboration)
People |
ORCID iD |
Gavin Kelsey (Principal Investigator) |
Publications
Wolodko K
(2020)
Leptin Resistance in the Ovary of Obese Mice is Associated with Profound Changes in the Transcriptome of Cumulus Cells.
in Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology
Veselovska L
(2015)
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.
in Genome biology
Tucci V
(2019)
Genomic Imprinting and Physiological Processes in Mammals
in Cell
Stewart KR
(2015)
Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.
in Genes & development
Stewart KR
(2016)
Establishment and functions of DNA methylation in the germline.
in Epigenomics
Smallwood SA
(2014)
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
in Nature methods
Sendžikaite G
(2019)
A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice.
in Nature communications
Saucedo-Cuevas L
(2023)
Genome-wide assessment of DNA methylation alterations induced by superovulation, sexual immaturity and in vitro follicle growth in mouse blastocysts.
in Clinical epigenetics
Title | MOESM1 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 1: Figure S1. Correlation matrix showing that all the replicates were highly correlated (100-CpG window size tiles; value between 0 and 100 in all 16 samples; n = 195,170). |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM1_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM1 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 1: Figure S1. Correlation matrix showing that all the replicates were highly correlated (100-CpG window size tiles; value between 0 and 100 in all 16 samples; n = 195,170). |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM1_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM2 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 2: Figure S2. The box-whisker plots show the global DNA methylation average of probes informative in all 16 individual datasets at different genomic features: A) Intragenic regions (n = 20,474); B) intergenic regions (n = 18,245); C) promoters (n = 7704). In the plots the line across the middle of the box shows the median, the upper and lower extremities of the box show the 25th and 75th percentile of the set of data, and the upper and lower black whiskers show the median plus/minus the interquartile (25-75%) range multiplied by 2. Individual points which fall outside this range are shown as filled circles, and they represent single outliers tiles. D) DNA methylation levels at repetitive elements showing the mean ± SEM. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM2_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM2 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 2: Figure S2. The box-whisker plots show the global DNA methylation average of probes informative in all 16 individual datasets at different genomic features: A) Intragenic regions (n = 20,474); B) intergenic regions (n = 18,245); C) promoters (n = 7704). In the plots the line across the middle of the box shows the median, the upper and lower extremities of the box show the 25th and 75th percentile of the set of data, and the upper and lower black whiskers show the median plus/minus the interquartile (25-75%) range multiplied by 2. Individual points which fall outside this range are shown as filled circles, and they represent single outliers tiles. D) DNA methylation levels at repetitive elements showing the mean ± SEM. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM2_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM3 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 3: Figure S3. Pie-charts showing the distribution of tiles overlapping gene bodies and promoters in the total informative tiles, hypomethylated tiles and hypermethylated tiles in IFC vs. SO, SO vs. SOA and SOA vs. IV comparisons. Differences were evaluated using Chi-square test and considered significant when p |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM3_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM3 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 3: Figure S3. Pie-charts showing the distribution of tiles overlapping gene bodies and promoters in the total informative tiles, hypomethylated tiles and hypermethylated tiles in IFC vs. SO, SO vs. SOA and SOA vs. IV comparisons. Differences were evaluated using Chi-square test and considered significant when p |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM3_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM4 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 4: Figure S4. SeqMonk screenshots of the DNA methylation profiles of the hypomethylated loci Myo16 (A, 13 tiles with more than 20% methylation difference) and Elt4 (B, 14 tiles with more than 20% methylation difference) in IFC compared to SO. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM4_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM4 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 4: Figure S4. SeqMonk screenshots of the DNA methylation profiles of the hypomethylated loci Myo16 (A, 13 tiles with more than 20% methylation difference) and Elt4 (B, 14 tiles with more than 20% methylation difference) in IFC compared to SO. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM4_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM5 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 5: Figure S5. SeqMonk screenshots of the DNA methylation profiles of the hypermethylated loci Prdm16 (A, 7 tiles with more than 20% methylation difference) and Soga1 (B, 6 tiles with more than 20% methylation difference) in IFC compared to SO. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM5_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM5 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 5: Figure S5. SeqMonk screenshots of the DNA methylation profiles of the hypermethylated loci Prdm16 (A, 7 tiles with more than 20% methylation difference) and Soga1 (B, 6 tiles with more than 20% methylation difference) in IFC compared to SO. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM5_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM6 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 6: Figure S6. SeqMonk screenshots of the DNA methylation profiles of the hypermethylated loci Zfp521 (A, 26 tiles with more than 20% methylation difference) and Atrnl1 (B, 22 tiles with more than 20% methylation difference) in SO compared to SOA. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM6_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM6 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 6: Figure S6. SeqMonk screenshots of the DNA methylation profiles of the hypermethylated loci Zfp521 (A, 26 tiles with more than 20% methylation difference) and Atrnl1 (B, 22 tiles with more than 20% methylation difference) in SO compared to SOA. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. Genes and oocyte mRNA are shown in red or blue depending on their direction of transcription (forward or reverse, respectively). The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM6_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM7 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 7: Figure S7. SeqMonk screenshots of the DNA methylation distribution at gene structure of ten important maternal effect proteins for DNA methylation establishment and maintenance. The location of the gene and the direction of transcription it is represented with the arrows. The promoter of the oocyte transcript is marked with a black star on the TSS (transcription start site) track. The data for the replicates is combined into the tracks labeled IFC, SO, SOA and IV. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM7_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Title | MOESM7 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 7: Figure S7. SeqMonk screenshots of the DNA methylation distribution at gene structure of ten important maternal effect proteins for DNA methylation establishment and maintenance. The location of the gene and the direction of transcription it is represented with the arrows. The promoter of the oocyte transcript is marked with a black star on the TSS (transcription start site) track. The data for the replicates is combined into the tracks labeled IFC, SO, SOA and IV. Each color-coded bar represents the methylation value of a non-overlapping 100-CpG tile. The track labeled mRNA represents the oocyte transcriptome annotaton from Veselovska et al. [24]. |
Type Of Art | Film/Video/Animation |
Year Produced | 2019 |
URL | https://springernature.figshare.com/articles/MOESM7_of_Genome-wide_assessment_of_DNA_methylation_in_... |
Description | ESPE Research Fellowship |
Amount | € 124,000 (EUR) |
Organisation | European Society of Pediatric Endocrinology (ESPE) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 01/2014 |
End | 12/2015 |
Description | Epigenome patterning in oocytes and its legacies in the embryo |
Amount | £1,964,775 (GBP) |
Funding ID | MR/S000437/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2018 |
End | 07/2025 |
Description | Post-doctoral travelling fellowship |
Amount | € 49,000 (EUR) |
Organisation | Academy of Finland |
Sector | Public |
Country | Finland |
Start | 08/2013 |
End | 08/2015 |
Description | Royal Society International Exchange Cost Share Programme |
Amount | £11,915 (GBP) |
Funding ID | IEC\R3\170052 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 03/2018 |
End | 03/2020 |
Title | High through-put single-cell DNA methylation profiling |
Description | We have improved our previously published method of profiling DNA methylation genome-wide in single cells (Smallwood et al., Nat. Methods 2014), by implementing the method on a liquid handing robot (Clark et al. Nat. Protocols 2017), which is allowing much higher through-put applications. An extensive protocol is provided. |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Allowing much higher through-put applications. |
Title | Parallel analysis of DNA methylation, chromatin accessibility, RNA expression in single mammalian cells |
Description | By combining previous single-cells we and others have developed, this new Method, term scNMT-seq, enables high-coverage, genome-wide profiling of DNA methylation, chromatin accessibility and RNA transcripts in parallel in single cells. |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Very recently published; too soon to identify notable impacts |
Title | Single-cell BS-seq |
Description | We developed a method to profile DNA methylation genome-wide in single cells, which has now been published (Smallwood et al., Nat. Methods 2014). This capability could have widespread application in assessing DNA methylation in rare cells (e.g., human gametes, preimplantation embryos), to assess DNA methylation heterogeneity amongst cells, which could be an important mechanism in developmental decisions, aging and pathological states, notably in cancer. |
Type Of Material | Technology assay or reagent |
Year Produced | 2014 |
Provided To Others? | Yes |
Impact | The development of this method has led to the establishment of new collaborations for our group. It has also been a key component underpinning the award of a Wellcome Trust Strategic Award by a consortium headed by my colleague Prof. W. Reik. |
Title | Ultra-low cell histone modification profiling |
Description | Optimised method for ultra-low cell native ChIP-seq for histone modifications, exemplified by use in 250 mouse oocytes (see Hanna et al. 2019 Nat. Struct. Mol. Biol.) |
Type Of Material | Technology assay or reagent |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | This is providing us with major new capability in profiling histone modifications reproducibly and quantitatively in biological samples such as mouse oocytes and mouse pre-implantation and early post-implantation embryos, and is now being applied for a variety of research questions by the group. We are also using the method in a number of collaborators and have trained others in the method. |
Title | Additional file 2 of Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes |
Description | Additional file 2: Table S1. Sequencing output for PBAT libraries. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Oxygen_concentration_affec... |
Title | Additional file 2 of Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes |
Description | Additional file 2: Table S1. Sequencing output for PBAT libraries. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Oxygen_concentration_affec... |
Title | Additional file 3 of Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes |
Description | Additional file 3: Table S2. CGIs overlapping promoter, intragenic and intergenic regions of methylated non-common CGIs after the comparison with the hypermethylated domains defined in Kdm1a oocytes and the CGIs methylated >25% in normoxia or 20% O2 CON, and >10% in MAO, LiCl and MAO+LiCl. PA promoter, Intra intragenic and Inter intergenic. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Oxygen_concentration_affec... |
Title | Additional file 3 of Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes |
Description | Additional file 3: Table S2. CGIs overlapping promoter, intragenic and intergenic regions of methylated non-common CGIs after the comparison with the hypermethylated domains defined in Kdm1a oocytes and the CGIs methylated >25% in normoxia or 20% O2 CON, and >10% in MAO, LiCl and MAO+LiCl. PA promoter, Intra intragenic and Inter intergenic. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Oxygen_concentration_affec... |
Title | Chromatin modifications during mouse oogenesis |
Description | High quality native ChIP-seq datasets for histone modifications H3K4me3, H3K27ac, H3K27me3 during oocyte growth and fully grown oocytes in the mouse. ChIP-seq datasets for H3K4me3 in oocytes genetically deficient in DNA methylation (Dnmt3a/Dnmt3b nulls). ChIP-seq datasets for oocytes genetically deficient in the major H3K4 methyltransferase MLL2 (KMT2B). Published in Hanna et al. Nat. Struct. Mol. Biol. 2018 |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Recently released datasets, too early to identify impact outside of research group. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93941GSE93941 |
Title | DNA methylation analysis of mouse oocytes after superovulation |
Description | Genome-wide DNA methylation datasets of mouse oocytes obtained after natural ovulation, superovulation or in vitro culture. Enables identification of genomic regions whose methylation may be susceptible to procedures associated with assisted reproduction techniques. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Published in Saenz-de-Juano et al. Clin Epigenetics 2019 PMID: 31856890 |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128656 |
Title | DNA methylation during mouse oogenesis |
Description | Genome-wide DNA methylation datasets by RRBS and PBAT from size-selected mouse oocytes during the oocyte growth phase. Published in Gahurova et al. 2017 Epigenetics and Chromatin. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Only recently released, impact outside of research group too early to say. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86297 |
Title | DNA methylation in Hira oocytes |
Description | Genome-wide, single-cell DNA methylation data from mouse oocytes lacking the histone chaperone HIRA, and associated controls, as reported in Nashun et al. 2015 Molecular Cell 60, 611-625. |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | Too soon to define notable impacts, as the accompanying paper, Nashun et al. 2015 Molecular Cell, was published in October 2015. |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66629 |
Title | DNA methylation in oocytes deficient in histone modifier |
Description | Genome-wide DNA methylation datasets (PBAT) and single-cell RNA-seq datasets from oocytes genetically deficient in the H3K4me3 methyltransferase MLL2 (KMT2B). Published in Hanna et al. 2018 Nat. Struct. Mol. Biol. |
Type Of Material | Database/Collection of data |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Recently released, too early to identify impact outside of research group. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93941GSE93941 |
Title | DNA methylation profiles of blastocysts after natural ovulation, superovulation or oocyte culture |
Description | Whole-genome DNA methylation datasets from individual mouse blastocysts derived from oocytes from natural ovulation, superovulation of in vitro follicle culture |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205097 |
Title | Epigenetic analysis of in vitro cultured mouse oocytes |
Description | DNA methylation (WGBS) and RNA-seq datasets from mouse oocytes cultured in vitro and in the presence of inhibitors histone demethylases or oocyte transcription factor |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
Impact | May help inform epigenetic safety in methods for in vitro maturation of gametes. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164864 |
Title | Epigenomic analysis of DNMT3A mutation |
Description | DNA methylation, gene expression and histone modification datasets from embryo and adult tissues from mouse strain carrying a point mutation in DNMT3A, which is associated with postnatal growth restriction. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | An analogous mutation in human DNMT3A has been identified to cause extreme primordial growth restriction and similar epigenetic changes. Our data published in Sendžikaite et al Nat Comms 2019 PMID: 31015495. |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117728 |
Title | Epigenomic analysis of mouse post-implantation embryos |
Description | Allellic DNA methylation, gene expression and histone modification datasets from embryonic tissues from mouse. Allows genome-wide identification of genes controlled by genomic imprinting, and distinction of imprinting conferred by DNA methylation or repressive chromatin in oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Published in Hanna et al. Genome Biol 2019 PMID: 31665063 |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124216 |
Title | Epigenomic analysis of oocytes lacking H3K4 methyltransferase SETD1B |
Description | H3K4me3 ChIP-seq and DNA methylation (WGBS) datasets from wild-type and Setd1b conditional knock-out mouse oocytes |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE167987 |
Title | Gene expression and DNA methylation variation with age in oocytes from mice |
Description | Parallel, single-cell genome-wide bisulphite-sequencing and RNA-sequencing datasets from oocytes from reproductively young and old mice (C57BL6/Babr) |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE154370 |
Title | Gene expression during mouse oogenesis |
Description | Deeply sequenced RNA-seq datasets from size-selected mouse oocytes during the oocyte growth phase. Published in Gahurova et al. 2017 Epigenetics and Chromatin. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | Only recently released, too early to identify impacts beyond research group. |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86297 |
Title | Human placental imprints |
Description | DNA methylation analysis of newly identified human placental-specific imprinted genes; published in Hanna et al., 2016 Genome Research doi:10.1101/gr.196139.115. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | Too soon to define notable impacts, as associated paper was published in Genome Research in January 2016. |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76263 |
Title | MOESM1 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 1 : Table S1: List of gDMR coordinates; list of ZFP57 binding sites in gDMRs; .xls, 25 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM1_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM1 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 1 : Table S1: List of gDMR coordinates; list of ZFP57 binding sites in gDMRs; .xls, 25 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM1_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM1 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 1: Table S1. Sequencing statistics for PBAT and RRBS libraries from size-selected oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM1_of_Transcription_and_chromatin_determina... |
Title | MOESM1 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 1: Table S1. Sequencing statistics for PBAT and RRBS libraries from size-selected oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM1_of_Transcription_and_chromatin_determina... |
Title | MOESM10 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 10: Table S3. Differentially hypomethylated tiles (n=829) and hypermethylated tiles (n=702) with more than 20% methylation difference in IFC compared to SO. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between IFC and SO (n=85). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM10_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM10 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 10: Table S3. Differentially hypomethylated tiles (n=829) and hypermethylated tiles (n=702) with more than 20% methylation difference in IFC compared to SO. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between IFC and SO (n=85). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM10_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM10 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 10: Table S9. PCR primers sequences for conventional bisulphite sequencing of selected CGIs. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM10_of_Transcription_and_chromatin_determin... |
Title | MOESM10 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 10: Table S9. PCR primers sequences for conventional bisulphite sequencing of selected CGIs. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM10_of_Transcription_and_chromatin_determin... |
Title | MOESM11 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 11: Table S4. Specific loci in IFC compared to SO that contained multiple differential hypo- or hypermethylated tiles (> 20% methylation difference). Enriched biological processes of hypomethylated genes in IFC compared to SO (n = 17), including the proteins involved in each GO term. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM11_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM11 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 11: Table S4. Specific loci in IFC compared to SO that contained multiple differential hypo- or hypermethylated tiles (> 20% methylation difference). Enriched biological processes of hypomethylated genes in IFC compared to SO (n = 17), including the proteins involved in each GO term. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM11_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM12 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 12: Table S5. Differentially hypomethylated tiles (n=110) and hypermethylated tiles (n=455) with more than 20% methylation difference in SOA compared to IV. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between SOA and IV (n=60). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM12_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM12 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 12: Table S5. Differentially hypomethylated tiles (n=110) and hypermethylated tiles (n=455) with more than 20% methylation difference in SOA compared to IV. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between SOA and IV (n=60). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM12_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM13 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 13: Table S6. Specific loci in SOA compared to IV that contained multiple differential hypo- or hypermethylated tiles (> 20% methylation difference). Enriched biological processes of hypermethylated promoters in SOA vs IV (20% difference of methylation, n=128). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM13_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM13 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 13: Table S6. Specific loci in SOA compared to IV that contained multiple differential hypo- or hypermethylated tiles (> 20% methylation difference). Enriched biological processes of hypermethylated promoters in SOA vs IV (20% difference of methylation, n=128). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM13_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM14 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 14: Table S7. Differentially hypomethylated tiles (n=48) and hypermethylated tiles (n=2031) with more than 20% methylation difference in SO compared to SOA. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between SO and SOA (n=107) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM14_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM14 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 14: Table S7. Differentially hypomethylated tiles (n=48) and hypermethylated tiles (n=2031) with more than 20% methylation difference in SO compared to SOA. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. Differentially methylated CGIs between SO and SOA (n=107) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM14_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM15 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 15: Table S8. Specific loci in SO vs. SOA comparison that contained multiple differential hypo- or hypermethylated tiles (more than 20% methylation difference). Enriched biological processes of hypermethylated genes in SO compared to SOA (n=40), including the proteins involved in each GO term. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM15_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM15 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 15: Table S8. Specific loci in SO vs. SOA comparison that contained multiple differential hypo- or hypermethylated tiles (more than 20% methylation difference). Enriched biological processes of hypermethylated genes in SO compared to SOA (n=40), including the proteins involved in each GO term. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM15_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM16 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 16: Table S9. Differentially hypomethylated tiles (n=4158) and hypermethylated tiles (n=3477) with more than 20% methylation difference in IFC compared to SOA. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM16_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM16 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 16: Table S9. Differentially hypomethylated tiles (n=4158) and hypermethylated tiles (n=3477) with more than 20% methylation difference in IFC compared to SOA. Each tile contains information about the genome location, overlapping gene, Ensembl ID, gene description and methylation percentage in each sample. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM16_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM17 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 17: Table S10. Specific loci in IFC vs. SOA comparison that contained multiple differential hypo- or hypermethylated tiles (more than 20% methylation difference). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM17_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM17 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 17: Table S10. Specific loci in IFC vs. SOA comparison that contained multiple differential hypo- or hypermethylated tiles (more than 20% methylation difference). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM17_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM18 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 18: Table S11. Genes commonly hypermethylated or hypomethylated in all pairwise comparisons. Enriched biological processes of genes commonly affected in the SO vs. SOA and IFC vs. SOA comparisons related to sexual maturity of oocytes (n=352). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM18_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM18 of Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity |
Description | Additional file 18: Table S11. Genes commonly hypermethylated or hypomethylated in all pairwise comparisons. Enriched biological processes of genes commonly affected in the SO vs. SOA and IFC vs. SOA comparisons related to sexual maturity of oocytes (n=352). |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM18_of_Genome-wide_assessment_of_DNA_methylation_in... |
Title | MOESM2 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 2 : Table S2: Pyrosequencing primer sequences; .xls, 12 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM2_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM2 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 2 : Table S2: Pyrosequencing primer sequences; .xls, 12 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM2_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM2 of Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues |
Description | Additional file 2. Supplementary Tables S1-S6. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM2_of_Endogenous_retroviral_insertions_drive_non-ca... |
Title | MOESM2 of Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues |
Description | Additional file 2. Supplementary Tables S1-S6. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM2_of_Endogenous_retroviral_insertions_drive_non-ca... |
Title | MOESM2 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 2: Table S2. Methylation levels of all CpGs and various genomic features that become methylated in GV oocytes in NGO, 60-65 µm and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM2_of_Transcription_and_chromatin_determina... |
Title | MOESM2 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 2: Table S2. Methylation levels of all CpGs and various genomic features that become methylated in GV oocytes in NGO, 60-65 µm and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM2_of_Transcription_and_chromatin_determina... |
Title | MOESM4 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 4 : Table S3. Summary of statistical analysis in Figures and Supplementary Figures; .xls, 24 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM4_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM4 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 4 : Table S3. Summary of statistical analysis in Figures and Supplementary Figures; .xls, 24 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM4_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM4 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 4: Table S3. CG, CHG and CHH methylation levels in NGO, 60-65 µm and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM4_of_Transcription_and_chromatin_determina... |
Title | MOESM4 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 4: Table S3. CG, CHG and CHH methylation levels in NGO, 60-65 µm and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM4_of_Transcription_and_chromatin_determina... |
Title | MOESM5 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 5 : Table S4. Hypomethylated regions in KHDC3Lc.1A>G mole; .xls, 56 KB |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM5_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM5 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 5 : Table S4. Hypomethylated regions in KHDC3Lc.1A>G mole; .xls, 56 KB |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM5_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM5 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 5: Table S4. Sequencing statistics for ssRNA-seq libraries from NGO, size-selected and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM5_of_Transcription_and_chromatin_determina... |
Title | MOESM5 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 5: Table S4. Sequencing statistics for ssRNA-seq libraries from NGO, size-selected and GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM5_of_Transcription_and_chromatin_determina... |
Title | MOESM6 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 6 : Table S5. DNA methylation sequencing summary; .xls, 10 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM6_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM6 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation |
Description | Additional file 6 : Table S5. DNA methylation sequencing summary; .xls, 10 KB. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM6_of_A_KHDC3L_mutation_resulting_in_recurr... |
Title | MOESM6 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 6: Table S5. Numbers of genes detected in ssRNA-seq libraries. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM6_of_Transcription_and_chromatin_determina... |
Title | MOESM6 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 6: Table S5. Numbers of genes detected in ssRNA-seq libraries. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM6_of_Transcription_and_chromatin_determina... |
Title | MOESM7 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 7: Table S6. Genes up-regulated =50 from e18.5 to 10-30 µm oocytes and from E18.5 to GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM7_of_Transcription_and_chromatin_determina... |
Title | MOESM7 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 7: Table S6. Genes up-regulated =50 from e18.5 to 10-30 µm oocytes and from E18.5 to GV oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM7_of_Transcription_and_chromatin_determina... |
Title | MOESM8 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 8: Table S7. Output from DREME analysis of sequence motifs differentially represented in early- and late-methylating CpG islands. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM8_of_Transcription_and_chromatin_determina... |
Title | MOESM8 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 8: Table S7. Output from DREME analysis of sequence motifs differentially represented in early- and late-methylating CpG islands. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM8_of_Transcription_and_chromatin_determina... |
Title | MOESM9 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 9: Table S8. Expression levels of transcription factors with binding motifs enriched in CGIs with low methylation level in 60-65 µm oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM9_of_Transcription_and_chromatin_determina... |
Title | MOESM9 of Transcription and chromatin determinants of de novo DNA methylation timing in oocytes |
Description | Additional file 9: Table S8. Expression levels of transcription factors with binding motifs enriched in CGIs with low methylation level in 60-65 µm oocytes. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/dataset/MOESM9_of_Transcription_and_chromatin_determina... |
Title | Multi-omic analyses of oocytes lacking H3K9 methyltransferases EHMT1/2 |
Description | H3K9me3 ChIP-seq, DNA methylation (WGBS) and RNA-seq datasets from wild-type and Ehmt1&2 conditional knock-out mouse oocytes |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE191026 |
Title | Multi-omic analyses of oocytes lacking H3K9 methyltransferases EHMT1/2 - proteomics |
Description | Proteomics datasets from wild-type and Ehmt1&2 conditional knock-out mouse oocytes |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD030265 |
Title | Oocyte ChIP-seq datasets |
Description | ChIP-seq datasets for selected histone modifications in mouse growing oocytes. DNA methylation profiles of oocytes lacking the histone demethylases KDM1A, KDM1B. As reported in Stewart et al., 2015 Genes and Development, 29, 2449-2462 |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | Too soon to define notable impacts, as the associated manuscript was published in Genes and Development in December 2015 |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74549 |
Title | Oocyte transcriptome, mouse |
Description | Deep strand-specific RNA-seq to establish in-depth transcriptome of mouse oocytes, as reported in Veselovska et al., 2015 Genome Biology 16, 209 |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | The publication in Genome Biology associated with these datasets has already attracted >30 citations, suggesting a good level of uptake of the data by the research community. |
URL | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70116 |
Title | Single-cell DNA methylation profiles |
Description | Single-cell methylation datasets for mouse oocytes and ES cells were submitted to the Gene Expression Omnibus (GEO) under accession GSE56879. |
Type Of Material | Database/Collection of data |
Year Produced | 2014 |
Provided To Others? | Yes |
Impact | Too soon to comment |
Title | Single-cell RNA-seq from oocytes and preimplantation embryos |
Description | Single-cell RNA-seq from oocytes and preimplantation embryos to profile gene expression changes in human preimplantation development |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | https://www.ncbi.nlm.nih.gov/bioproject/?term=630371 |
Title | Single-cell multi-omics data from human pre-implantation embryos |
Description | Single-cell RNA-seq and BS-seq datasets from arrested human pre-implantation embryos |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
Impact | Too early to say |
URL | https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA630371 |
Description | Analysis of Mll2-deficient oocytes |
Organisation | Technical University of Dresden |
Department | Biotechnology Center |
Country | Germany |
Sector | Academic/University |
PI Contribution | We framed the biological question and were responsible for experimental design and data analysis. We performed DNA methylation and histone modification analysis of oocytes conditionally deleted for Mll2 provided by the partner. |
Collaborator Contribution | Provided mice with conditional knock-out allele of Mll2 and Mll2-deficient oocytes. |
Impact | Joint publication: Hanna et al., Nat. Struct. Mol. Biol. 2018. Deposited sequence datasets at NCBI GEO: GSE93941. |
Start Year | 2013 |
Description | Analysis of Setd1b-deficient oocytes |
Organisation | Technical University of Dresden |
Department | Biotechnology Center |
Country | Germany |
Sector | Academic/University |
PI Contribution | We performed analysis of RNA-seq datasets in oocytes conditionally deleted for Setd1b generated by the partner, with reference to our mouse oocyte transcriptome assemblies (Veselovska et al., 2015 Genome Biol; Gahurova et al., 2017 Epigenetics & Chromatin). |
Collaborator Contribution | Partner was responsible for framing the project and experimental design and providing data from mice with conditional knock-out allele of Setd1b in oocytes |
Impact | Joint publication: Brici et al., Development 2017 |
Start Year | 2013 |
Description | Analysis of histone modifications in mice with loss-of-imprinting of Zac1 |
Organisation | Clermont Université |
Country | France |
Sector | Academic/University |
PI Contribution | Our group was responsible for framing the project and experimental design; we provided tissues from mice with loss-of-imprinting of Zac1. |
Collaborator Contribution | Their group performed ChIP-PCR analysis in tissues from Zac1 loss-of-imprinting mice we provided. |
Impact | Joint publication Veselovska et al. 2015 Genome Biol. |
Start Year | 2013 |
Description | Bioinformatic analysis of oocyte ChIP-seq data |
Organisation | Helmholtz Zentrum München |
Department | Institute of Computational Biology |
Country | Germany |
Sector | Private |
PI Contribution | We provided ChIP-seq datasets for various histone modifications in mouse wild-type and genetic knock-out oocytes to enable partner to test new informatics tools they had developed. |
Collaborator Contribution | The partner provided new informatics methods, based on multivariate Hidden-Markov Models, to enable analysis of multiple ChIP-seq datasets, with focus on multivariate comparisons. |
Impact | Joint publication: Hanna et al., Nat. Struct. Mol. Biol. 2018. Deposited sequence datasets at NCBI GEO: GSE93941. Hosted visiting bioinformatics PhD student from collaborating lab. Inter-disciplinarity: partner provides modelling and informatics expertise, our group provides biological datasets. |
Start Year | 2016 |
Description | Bioinformatic analysis of single-cell epigenomic datasets |
Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | My group, together with the group of my colleague Wofl Reik, have developed methods for single-cell profiling of DNA methylation, upon which we have combined single-cell RNA-seq and single-cell profiling of chromatin accessibility. We have provided datasets from mouse ES cells and oocytes which the partner has explored and developed bioinformatic methods for investigating epigenetic heterogeneity. |
Collaborator Contribution | The partner has provided high level bioinformatic expertise. |
Impact | This has led to four published papers so far: Smallwood et al. 2014 Nat. Methods; Angermueller et al. 2016 Nat. Methods; Kelsey et al. 2017 Science; Clark et al. 2018 Nat. Comms. The multidisciplinarity is the combination of developmental epigenetics and bioinformatics. |
Start Year | 2014 |
Description | Chromatin remodelling in oocytes |
Organisation | Technical University of Dresden |
Country | Germany |
Sector | Academic/University |
PI Contribution | Project concept, data generation, data analysis |
Collaborator Contribution | sample generation, data analysis |
Impact | Joint publication: PMID: 35137160 |
Start Year | 2010 |
Description | DNA methylation analysis in oocytes genetically deficient for Kdm1a (Lsd1) and Kdm1b (Aof1) |
Organisation | University of Texas |
Department | M. D. Anderson Cancer Center |
Country | United States |
Sector | Academic/University |
PI Contribution | We were responsible for framing the project and experimental design and performed genome-wide DNA methylation analysis in oocytes genetically deficient in the H3K4me2 demethylases KDM1A or KDM1B, provided by the collaborating group. |
Collaborator Contribution | The partner provided oocytes from mice genetically deficient in Kdm1a or Kdm1b; provided RNA-seq datasets for these oocytes. |
Impact | Joint publications Stewart et al., 2015 Genes & Dev; Gahurova et al. 2017 Epigenetics & Chromatin. Deposited sequence datasets at NCBI GEO: GSE73803 and GSE74549. |
Start Year | 2011 |
Description | DNA methylation analysis in oocytes genetically deficient in Hira |
Organisation | Medical Research Council (MRC) |
Department | MRC Clinical Sciences Centre (CSC) |
Country | United Kingdom |
Sector | Public |
PI Contribution | We performed single-cell, genome-wide bisulphite sequencing of oocytes deficient in H3.3 chaperone HIRA, provided by the collaborating group; using our newly established single-cell BS-seq method (Smallwood et al., 2014 Nat. Meths). |
Collaborator Contribution | The partner was responsible for framing the project and experimental design and provided mouse oocytes conditionally deleted in Hira. |
Impact | Joint publication Nashun et al. 2015 Mol. Cell. Deposited sequence datasets at NCBI GSE66629. |
Start Year | 2014 |
Description | DNA methylation analysis of human blastocysts obtained after IVM |
Organisation | Vrije Universiteit Brussel |
Country | Belgium |
Sector | Academic/University |
PI Contribution | Performed DNA methylation analysis and gene expression analysis in blastocysts from control ICSI or ICSI of oocytes obtained by in vitro maturation. |
Collaborator Contribution | Generated samples: IVM of donor oocytes, ICSI, blastocyst culture and collection. |
Impact | Joint publication Saenz-de-Juano et al. 2019 Hum Reprod 2019 PMID: 31398248 |
Start Year | 2014 |
Description | DNA methylation analysis of mouse oocytes after superovulation |
Organisation | Vrije Universiteit Brussel |
Country | Belgium |
Sector | Academic/University |
PI Contribution | Performed genome-wide DNA methylation analysis of mouse oocytes and blastocysts and bioinformatics analysis of datasets. |
Collaborator Contribution | Generated samples: mouse oocytes obtained after natural ovulation, superovulation or in vitro culture, as well as blastocysts derived from these embryos |
Impact | Joint publication Saenz-de-Juano et al. 2019 Clin Epigenetics PMID: 31856890 Joint publication Saucedo-Cuevas et al. 2023 Clin Epigenetics PMID: 36647174 Partners in further funding: H2020 MCSA Innovative Training Network EurOVA, awarded 2019 |
Start Year | 2016 |
Description | Identification of polymorphically imprinted loci in human placenta |
Organisation | University of British Columbia |
Country | Canada |
Sector | Academic/University |
PI Contribution | Our team analysed 450k array datasets from human placenta samples provided by the collaborating group. We also used targeted bisulphite sequencing to validate candidate imprinted loci identified by the array analysis. |
Collaborator Contribution | Their team was responsible for framing the project and experimental design and provided human placental DNA samples. |
Impact | Joint publication Hanna et al. 2016 Genome Res. Deposited sequence datasets at NCBI GEO GSE74738 and GSE76273 |
Start Year | 2015 |
Description | Multi-omics analysis of EHMT1/2-deficient oocytes |
Organisation | Cancer Research UK Cambridge Institute |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Project conception, sample generation, data analysis |
Collaborator Contribution | Generation of proteomics datasets from mouse oocytes and analysis |
Impact | Joint publication: Demond et al. 2023 Genome Res PMID: 36690445 Joint grant application submitted |
Start Year | 2019 |
Description | RNA and methylation analysis of oocytes and embryos |
Organisation | Bellvitge Biomedical Research Institute |
Country | Spain |
Sector | Academic/University |
PI Contribution | Single-cell RNA-seq and single-cell BS-seq of oocyte and preimplantation embryo samples from which to profile expression of candidate regulators of imprinting. |
Collaborator Contribution | Molecular and cell biology analysis of ;imprinting regulator ZFP57 and other candidate regulators; patient recruitment; sample generation. |
Impact | Joint publication: Monteagudo-Sanchez et al. 2020 PMID: 33053156 Joint grant application. |
Start Year | 2017 |
Description | Single-cell multi-omic analysis of human preimplantation embryos |
Organisation | Bellvitge Biomedical Research Institute |
Department | Cancer Epigenetics and Biology Programme |
Country | Spain |
Sector | Public |
PI Contribution | Generation of single-cell multi-omic datasets (RNA-seq, BS-seq) from human oocytes and single blastomeres of preimplantation embryos |
Collaborator Contribution | Project conception, sample generation, data analysis |
Impact | Joint publication: Hernandez Mora et al. 2023 Cell Reports PMID: 36763500 |
Start Year | 2017 |
Description | Single-cell multi-omic analysis of human preimplantation embryos |
Organisation | University of East Anglia |
Department | School of Biological Sciences UEA |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Generation of single-cell multi-omic datasets (RNA-seq, BS-seq) from human oocytes and single blastomeres of preimplantation embryos |
Collaborator Contribution | Project conception, sample generation, data analysis |
Impact | Joint publication: Hernandez Mora et al. 2023 Cell Reports PMID: 36763500 |
Start Year | 2017 |
Description | Babraham Schools Day |
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 | Schools |
Results and Impact | As part of the annual Babraham Schools' Day, my group hosted 5 GCSE and 5 A level students for half-day practical sessions in the lab. |
Year(s) Of Engagement Activity | 2017 |
Description | Babraham Schools Day |
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 | Schools |
Results and Impact | Annual event in which local GCSE and A-level students are hosted in my group and many other groups at the Institute for a day of practical demonstrations. |
Year(s) Of Engagement Activity | Pre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016 |
Description | Babraham Schools' Day |
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 | Schools |
Results and Impact | As part of the annual Babraham Schools' Day, my group hosted 5 GCSE and 5 A level students for half-day practical sessions in the lab. |
Year(s) Of Engagement Activity | 2018 |
Description | Cambridge Science Festival |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Type Of Presentation | Poster Presentation |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Presentation of of the Babraham Institute Epigenetics exhibit at the Cambridge Science Festival March 2013. A large number of interested public attended, viewed the exhibit and asked questions of me and the other presenters during the weekend event. Some very interesting and insightful questions from some visitors to the exhibit. |
Year(s) Of Engagement Activity | 2013 |
Description | GenomeWeb interview |
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 | Interview with GenomeWeb on the publication of our single-cell combined DNA methylation and transcriptome sequencing method published in Nature Methods (Angermueller et al. 2016). |
Year(s) Of Engagement Activity | 2016 |
Description | Local community visit - Pampisford Society |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | A society from the local community - the Pampisford Society - visited the Institute because of interest in finding out about the nature of the research conducted at the Institute. As well as a tour of some of the research facilities, including a virtual tool of the animal facilities, and presentations on the Institute, there were two research talks given, one by myself. The talk covered how we profile epigenetic marks in gametes and early embryos, and how we seek to understand possible effects of lifestyle (diet) and age on the transmission of epigenetic marks from parents to offspring. There was considerable interest in this area of research. |
Year(s) Of Engagement Activity | 2017 |
Description | Museums Week |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | Yes |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Many very stimulating discussions with members of the public at many levels who approached the exhibit. No tangible impacts beyond the perception that many of the people who visited the exhibit appeared to be interested to find out about epigenetics and will have left the exhibit more informed; there is substantial interest in epigenetics amongst many people, particularly after television programmes that have covered some of the ground. |
Year(s) Of Engagement Activity | 2014 |
Description | Press release - Keeping eggs fresh with epigenetics |
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 from Babraham to accompany publication of paper 'MLL2 conveys transcription-independent H3K4me3 in the oocyte', by Hanna et al. Nat. Struct. Mol. Biol. 2018. Picked up by 9 news outlets and blogs. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.babraham.ac.uk/news/2018/01/keeping-egg-cells-fresh-with-epigenetics |
Description | Press release - Molecular Cell paper |
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 associated with publication Nashun et al. 2015 Molecular Cell on role of nucleosome replacement in oocyte development. |
Year(s) Of Engagement Activity | 2015 |
Description | STEM teacher visit |
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 | Schools |
Results and Impact | As part of a week-long visit to the Institute, my group hosted 3 biology A-level teachers from local schools for involvement in practical work in the lab over a 2-day period. |
Year(s) Of Engagement Activity | 2016 |
Description | Talk to journalism students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | Keynote/Invited Speaker |
Geographic Reach | Regional |
Primary Audience | Undergraduate students |
Results and Impact | Presentation about the topic of this research award to ~15 journalism students from City University hosted at the Babraham Institute, March 2013. Some genuinely interested and insightful and informed questions from students interested in pursuing a career in science journalism. |
Year(s) Of Engagement Activity | 2013 |
Description | Teacher workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Talk to sixth-form teachers as part of 'Twilight Teacher Session', held at the Wellcome Trust Sanger Institute, Hinxton. The remit of the event was to inform teachers about state-of-the-art DNA sequencing technologies and their applications. It comprised a tour of sequencing facilities at the Sanger and a talk from a Sanger scientist and from myself, in which I presented current progress in single-cell sequencing methods and their applications in reproductive medicine. The workshop also discussed teaching aids that could be used to illustrate current sequencing capabilities. |
Year(s) Of Engagement Activity | 2017 |