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Sample GSM2041080 Query DataSets for GSM2041080
Status Public on Sep 15, 2016
Title ChIP-Seq E5.5 epiblast K27Me3
Sample type SRA
 
Source name E5.5 epiblast
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK
tissue/cell type: E5.5 epiblast
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
Treatment protocol To isolate E5.5 or E6.5 epiblast and extraembryonic ectoderm, naturally mated female mice were sacrificed and embryos were dissected from uterus, decidua and Reichert’s membrane in a dish containing DMEM plus 10% FBS. Carefully cut off ectoplacental cone using syringe needle and subject embryos to pancreatic and trypsin enzyme digestion for 2~3 minutes. Embryos were recovered 5 minutes in DMEM medium plus 10% FBS. Gently suck and blow the embryo into a capillary pipet to remove the visceral endoderm and then cut off epiblast and extraembryonic ectoderm along the boundary of embryonic and extraembryonic region using syringe needle.
Extracted molecule genomic DNA
Extraction protocol embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.
 
Submission date Jan 18, 2016
Last update date May 15, 2019
Contact name Bingjie Zhang
Organization name Tsinghua University
Street address 30 Shuangqing Rd
City Beijing
State/province Beijing
ZIP/Postal code 100190
Country China
 
Platform ID GPL18480
Series (1)
GSE76687 Resetting epigenetic memory by reprogramming of histone modifications in mammals
Relations
BioSample SAMN04419969
SRA SRX1533829

Supplementary file Size Download File type/resource
GSM2041080_E5.5_epiblast_k27me3.bed.gz 38.2 Mb (ftp)(http) BED
GSM2041080_E5.5_epiblast_k27me3_broadpeak.bed.gz 136.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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