GSE59738
H3K4me3 Epigenomic Landscape derived from ChIP-Seq of 1,000 mouse early embryonic cells
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. Overall design: 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