|
| Status |
Public on May 26, 2021 |
| Title |
Hdac3fl/+ RS input for control H3K9ac |
| Sample type |
SRA |
| |
|
| Source name |
round spermatids (RS)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: round spermatids (RS)
genotype: wild type
strain: C57BL/6
chip antibodies: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were sonicated, antibody-bound DNA complexes were immunoprecipitated, washed, and DNA was extracted.
DNA was amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ChIP-seq reads were aligned to the mouse genome (mm10) using BOWTIE software (bowtie2 version 2.3.4.3)
The aligned reads were further filtered to remove those with low mapping quality and duplicated arising as an artefact of sample amplification or sequencing
Peak calling was carried out by using MACS2 (version 2.1.2, with options'-mfold 5, 50 –p 0.0001') on ChIP file against the input file.
Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
May 26, 2021 |
| Contact name |
Lan Ye |
| Organization name |
Nanjing Medical University
|
| Street address |
B112 Xuehai Building,101 Longmian Avenue, Jiangning district
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
211166 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE153063 |
Changes of H3K9ac and H3K27ac recruitment in pachytene spermatocytes and round spermatids from testes-specific HDAC3-depleted mice and genome-wide maps of HDAC3,NCOR and Sox30 in wild-type and Sox30 KO testes |
| GSE153065 |
Changes of H3K9ac and H3K27ac recruitment and gene expression in pachytene spermatocytes and round spermatids depleted of HDAC3 |
|
| Relations |
| BioSample |
SAMN15351367 |
| SRA |
SRX8602974 |
