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Sample GSM1845284 Query DataSets for GSM1845284
Status Public on Sep 15, 2016
Title ChIP-Seq 5000 mESC K4Me3
Sample type SRA
 
Source name Embryonic stem cell
Organism Mus musculus
Characteristics strain: R1
developmental stage: Embryonic stem cell
chip antibody: custom-made H3K4Me3 antibody (Abmart)
Treatment protocol Mouse ES cells were cultured without irradiated mouse embryonic fibroblasts (MEFs) in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, counted cells were lysed for STAR ChIP-seq or Smart-seq2.
Growth protocol mESCs were cultured routinely in LIF and serum medium.
Extracted molecule genomic DNA
Extraction protocol After washing with PBS, mESCs were incubated in lysis buffer
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. 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 Aug 06, 2015
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)
GSE71434 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
Relations
SRA SRX1134821
BioSample SAMN03979653

Supplementary file Size Download File type/resource
GSM1845284_5000_mESC_K4me3.bed.gz 27.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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