|
| Status |
Public on Jul 17, 2020 |
| Title |
PS H3K9me3 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
testis
|
| Organism |
Mus musculus |
| Characteristics |
tissue: testis
cell type: pachytene spermatocytes
development stage: 6-8 weeks
chip antibody: H3K9me3 (Active Motif, 39161)
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All sorted cells and H3K9me3 antibody incubated by magnetic beads were immunoprecipitated and DNA was finally isolated. The amount of DNA used for the ChIP: 6pg.
The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer's instructions. Paired-end 150-bp sequencing was performed on Illumina HiSeq X10.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ploidy: 4N
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, low quality. The processed reads were then aligned to the mouse genome (mm9) with bowtie2 (version 2.2.9) with default settings.
Peaks were called using macs14(v1.4.2) with the parameters "macs14 -g mm --nomodel --nolambda --shiftsize=73" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 callpeak function and normlized to one million eads per sample using --SPMR option. Scores represent normalized tag counts per million reads.
|
| |
|
| Submission date |
Sep 19, 2019 |
| Last update date |
Jul 18, 2020 |
| Contact name |
liu ying dong |
| E-mail(s) |
liuyingdong2017@126.com
|
| Phone |
18729187605
|
| Organization name |
Northwest University of Agriculture and Forestry Science and Technology
|
| Department |
College of Animal Science and Technology
|
| Lab |
Zeng wenxian
|
| Street address |
Shaanxi
|
| City |
Xi'an, Shaanxi |
| ZIP/Postal code |
710000 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE137742 |
Ultra-low-input native ChIP-seq data of four germ-cell types during mouse spermatogenesis |
| GSE137744 |
ltra-low-input native ChIP-seq and Whole genome bisulfite Sequencing data of four types mouse spermatogenesis |
|
| Relations |
| BioSample |
SAMN12788960 |
| SRA |
SRX6874370 |
