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Sample GSM2205867 Query DataSets for GSM2205867
Status Public on Sep 15, 2016
Title ChIP-Seq sperm K4Me3 rep2
Sample type SRA
Source name Sperm
Organism Mus musculus
Characteristics strain: PWK
tissue: sperm
chip antibody: custom-made H3K4Me3 antibody
chip antibody vendor: Abmart
Treatment protocol Dissect the caudal epididymi from adult males. Make small cuts in each epididymis. Add 3 ml of Donners medium and incubate the tube at 37 °C for 1 h. Collect the upper 2.5 ml of the liquid from each tube. Spin the mixture at 2,500g for 6 min at 4 °C and discard the supernatant
Extracted molecule genomic DNA
Extraction protocol Pure sperm were treated with DTT and NEM
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
Description processed data files: sperm_K4me3_broadpeak.bed.gz
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 Jun 20, 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)
GSE71434 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development
BioSample SAMN05272495
SRA SRX1865244

Supplementary file Size Download File type/resource
GSM2205867_sperm_K4me3_rep2.bed.gz 58.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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