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H3K4me3 Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells

ABSTRACT: Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful tool to dissect global epigenetic landscapes of cells. However, this method usually consumes millions of cells. Here we develop a robust technique for performing ChIP-Seq using as low as 1,000 cells. This method combines a semi-automatic nanoliter ChIP reaction with a carrier-based sequencing library preparation strategy without pre-amplifying the ChIP product. We used this method to investigate the pattern of trimethylation of histone 3 lysine 4 (H3K4me3) of mouse post-implantation epiblast cells at embryonic day 6.5 (E6.5) and showed that it is more similar to that of mouse Epi-Stem cells (mEpiSCs) than that of mouse Embryonic Stem cells (mESCs). Together with the high similarity between the transcriptomes of EpiSCs and E6.5 epiblast cells, this suggests that mEpiSCs is a reliable in vitro model for post-implantation epiblast cells in vivo.

ORGANISM(S): Mus musculus

PROVIDER: GSE59738 | GEO | 2015/07/24

SECONDARY ACCESSION(S): PRJNA256084

REPOSITORIES: GEO

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H3K4me3 Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells

Project description:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful tool to dissect global epigenetic landscapes of cells. However, this method usually consumes millions of cells. Here we develop a robust technique for performing ChIP-Seq using as low as 1,000 cells. This method combines a semi-automatic nanoliter ChIP reaction with a carrier-based sequencing library preparation strategy without pre-amplifying the ChIP product. We used this method to investigate the pattern of trimethylation of histone 3 lysine 4 (H3K4me3) of mouse post-implantation epiblast cells at embryonic day 6.5 (E6.5) and showed that it is more similar to that of mouse Epi-Stem cells (mEpiSCs) than that of mouse Embryonic Stem cells (mESCs). Together with the high similarity between the transcriptomes of EpiSCs and E6.5 epiblast cells, this suggests that mEpiSCs is a reliable in vitro model for post-implantation epiblast cells in vivo. Use 1 million mEpiSCs and 1million mESCs as the positive control, 1000 mEpiSC and 1000 mESCs samples are used to validate the protocol. 1000 mEpiblasts have two biological replicates

2015-07-24 | E-GEOD-59738 | biostudies-arrayexpress

Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells

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