|
| 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 |
|
| Relations |
| BioSample |
SAMN05272495 |
| SRA |
SRX1865244 |
