GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2041066 Query DataSets for GSM2041066
Status Public on Sep 15, 2016
Title ChIP-Seq PWK sperm K27Me3
Sample type SRA
Source name Mature sperm
Organism Mus musculus
Characteristics strain: PWK
tissue/cell type: Mature sperm
chip antibody: H3K27Me3
chip antibody vendor: Diagenode
chip antibody cat. #: C15410069; pAb-069-050
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. (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
BioSample SAMN04419955
SRA SRX1533815

Supplementary file Size Download File type/resource
GSM2041066_Sperm_k27me3.bed.gz 60.6 Mb (ftp)(http) BED
GSM2041066_Sperm_k27me3_broadpeak.bed.gz 123.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap