ATACseq
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001007166 | EGA |
REPOSITORIES: EGA
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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 Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity.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
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Project description:Early embryo development is a dynamic process involving important molecular and structural changes leading to the embryonic genome activation (EGA) and first cell lineage differentiation. Our aim was to elucidate proteomic changes in bovine embryos developed in vivo. Eleven Holstein females were used as embryo donors and pools of embryos at the 4-6 cell, 8-12 cell, morula, compact morula and blastocyst stages were analyzed by nanoliquid chromatography coupled with tandem MS (nanoLC-MS/MS). A total of 2757 proteins were identified, of which 1950 were quantitatively analyzed. Principal component analysis of data showed a separation of embryo pools according to their developmental stage. Differentially abundant proteins (DAPs) between stages were clustered into 626 upregulated and 400 downregulated proteins with most significant changes at the time of EGA and blastocyst formation. The main pathways and processes overrepresented among upregulated proteins were RNA metabolism, protein translation and ribosome biogenesis whereas Golgi vesicle transport and protein processing in endoplasmic reticulum were overrepresented among downregulated proteins. This is the first comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo. These data provide a number of functional protein candidates and will be useful to evaluate the impact of in vitro conditions on embryo quality.
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