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Omics score: 1004

ERA-MC-AE

ABSTRACT: Organisation EGAO00000000239

PROVIDER: EGAO00000000239 | EGA |

REPOSITORIES: EGA

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Publications

Identifying genetic risk variants for coronary heart disease in familial hypercholesterolemia: an extreme genetics approach.

Versmissen Jorie J Oosterveer Daniëlla M DM Yazdanpanah Mojgan M Dehghan Abbas A Hólm Hilma H Erdman Jeanette J Aulchenko Yurii S YS Thorleifsson Gudmar G Schunkert Heribert H Huijgen Roeland R Vongpromek Ranitha R Uitterlinden André G AG Defesche Joep C JC van Duijn Cornelia M CM Mulder Monique M Dadd Tony T Karlsson Hróbjartur D HD Ordovas Jose J Kindt Iris I Jarman Amelia A Hofman Albert A van Vark-van der Zee Leonie L Blommesteijn-Touw Adriana C AC Kwekkeboom Jaap J Liem Anho H AH van der Ouderaa Frans J FJ Calandra Sebastiano S Bertolini Stefano S Averna Maurizio M Langslet Gisle G Ose Leiv L Ros Emilio E Almagro Fátima F de Leeuw Peter W PW Civeira Fernando F Masana Luis L Pintó Xavier X Simoons Maarten L ML Schinkel Arend F L AF Green Martin R MR Zwinderman Aeilko H AH Johnson Keith J KJ Schaefer Arne A Neil Andrew A Witteman Jacqueline C M JC Humphries Steve E SE Kastelein John J P JJ Sijbrands Eric J G EJ

European journal of human genetics : EJHG 20140611 3

Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), a disorder characterized by coronary heart disease (CHD) at young age. We aimed to apply an extreme sampling method to enhance the statistical power to identify novel genetic risk variants for CHD in individuals with FH. We selected cases and controls with an extreme contrast in CHD risk from 17,000 FH patients from the Netherlands, whose functional LDLR mutation was unequivocally established. ...[more]

PMID: 24916650

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Erasmus MC Cancer Institute, department of Hematology, Rotterdam, the Netherlands

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RNA-Seq of polyA mRNA from rare types of cultured or uncultured primary cells of different haemopoetic lineages from healthy individuals in the BLUEPRINT epigenome project (Expression Atlas tissue view)

Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 29 samples of primary cells or cultured primary cells of different haemopoeitc lineages from cord blood are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001165. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu

2015-09-30 | E-MTAB-3819 | biostudies-arrayexpress

RNA-Seq of polyA mRNA from plasma cells of tonsil from healthy individuals in the BLUEPRINT epigenome project

Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 4 samples of primary cells from tonsil with cell surface markes CD20med/CD38high in young individuals (3 to 10 years old) are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of EGA data sets is EGAD00001001523. Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. The mapping of samples to these EGA accessions can be found in the 'Sample Data Relationship Format' file of this ArrayExpress record. Information on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu

2016-05-12 | E-MTAB-4754 | biostudies-arrayexpress

Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [RNA-seq]

Project description:Reprogramming of histone modification regulates gene expression and mammal preimplantation development. Trimethylation of lysine 4 on histone 3 (H3K4me3) has unique landscape in mouse oocytes and early embryos. However, the dynamics and function of H3K4me3 in livestock embryos remain unclear. To address how it is reprogrammed in domestic animals, we profiled changes of H3K4me3 during bovine early embryo development. Notably, the overall signal of H3K4me3 decreased during embryonic genome activation (EGA). By utilizing ultra-low-input native ChIP-seq (ULI-NChIP-seq) technology, we observed widespread broad H3K4me3 domains in oocytes and embryos. The signal of broad H3K4me3 began to decrease after fertilization and was lowest after EGA. Along with the removal of broad H3K4me3, deposition of H3K4me3 at promoter regions enhanced gradually. Besides, the transcriptional activity and signal of promoter H3K4me3 showed positive correlation after the erasure of broad H3K4me3 at 16-cell stage. Moreover, knocking down of demethylases KDM5A, KDM5B and KDM5C caused EGA delay and blastocyst formation failure. RNA-seq analysis revealed 47.8% down-regulated genes in knockdown embryos at 8/16-cell stage were EGA genes, and 63.1% of up-regulated genes were maternal transcripts. Particularly, the positive correlation between transcriptional activity and promoter H3K4me3 during EGA was restrained when knocking down of KDM5A, KDM5B and KDM5C. Overall, our work initiatively mapped the genomic reprogramming of H3K4me3 during bovine preimplantation development, and KDM5A/B/C played roles in modulating oocyte-to-embryonic transition (OET) through timely erasure of broad H3K4me3 domains far away from promoters.

2022-03-31 | GSE189101 | GEO

Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [ChIP-seq]

2022-03-31 | GSE189100 | GEO

Strand-specific RNA-Seq of rRNA-depleted total RNA from common types of cultured or uncultured primary cells of different haemopoetic lineages from healthy individuals in the BLUEPRINT epigenome project

Project description:This experiment contains a subset of data from the BLUEPRINT Epigenome project ( http://www.blueprint-epigenome.eu ), which aims at producing a reference haemopoetic epigenomes for the research community. 74 samples of primary cells or cultured primary cells of different haemopoeitc lineages from cord blood, venous blood, bone marrow and thymus are included in this experiment. This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. There are 32 EGA data set accessions, which can be found under the Comment[EGA_DATA_SET] column in the 'Sample Data Relationship Format' (SDRF) file of this ArrayExpress record (http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3827/E-MTAB-3827.sdrf.txt). Details on how to apply for data access via the BLUEPRINT data access committee are on the EGA data set pages. Likewise, mapping of samples to these EGA accessions can be found in the SDRF file. Please note that the raw data files for 11 sequencing runs have yet been deposited at EGA, so they are marked with \\ot available\\ under the Comment[SUBMITTED_FILE_NAME] field in the SDRF file, and were included for the sake of completeness. Further iInformation on individual samples and sequencing libraries can also be found on the BLUEPRINT data coordination centre (DCC) website: http://dcc.blueprint-epigenome.eu\

2015-09-30 | E-MTAB-3827 | biostudies-arrayexpress

Fertilization triggers a transcription program mouse & human one-cell embryos

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Influence of in-vitro culture conditions and maternal metabolic status during embryonic genome activation on the Day-4 embryo transcriptome

Project description:Milk production during the early postpartum in dairy cows can impact the circulating metabolites and negatively affects embryo survival. However, the molecular consequences for the embryo during its development in the oviduct are still unknown. The objective was to determine the impact of metabolic status on embryonic genome activation (EGA) using high-throughput sequencing to generate comprehensive transcriptome profiles of bovine 16-cell stage embryos which had undergone EGA in vitro or in the oviducts of primiparous postpartum dry or postpartum lactating Holstein Friesian cows.

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