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| Status |
Public on Aug 19, 2024 |
| Title |
KGN-H3K27Ac-Ctrl-CHIP |
| Sample type |
SRA |
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| Source name |
ovarian
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| Organism |
Homo sapiens |
| Characteristics |
tissue: ovarian
cell line: KGN
cell type: immortalized human granulosa cell
genotype: H3K27AC
treatment: control
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| Treatment protocol |
10 um testosterone for 24 h
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| Growth protocol |
DMEM-F12 with 10% FBS
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked with a final concentration of 1.5% formaldehyde
TruSeq DNA LT/HT Sample Prep Kit (Illumina) and underwent quality control on the Bioanalyzer (Agilent 2200).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The ChIP-seq reads were aligned to the human genome mm10 using Bowtie (Version 2.0) with default parameters.
For peak calling, MACS2.0 was employed with default parameters and a significance threshold (q value cutoff = 0.05), as described previously,
To visualize the ChIP-seq data, deepTools2 was utilized, BAM coverage was used to generate the bigwig files.
The genome tracks were visualized in the software program IGV. in different samples.
Peak annotation was performed using R and the ChIPseeker package and bedtools were employed to analyze the overlapping regions
Assembly: hg38
Supplementary files format and content: excel, narrow peak
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| Submission date |
Jul 18, 2024 |
| Last update date |
Aug 19, 2024 |
| Contact name |
JIAMIN JIN |
| E-mail(s) |
11718252@zju.edu.cn
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| Phone |
18768117135
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| Organization name |
ZheJiang University
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| Street address |
QingChun East Road
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| City |
HangZhou |
| ZIP/Postal code |
310016 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE272605 |
testosterone application induced H3K27 deacetylation |
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| Relations |
| BioSample |
SAMN42594925 |
| SRA |
SRX25382434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8406607_ctrl-input_vs_ctrl-IP_peaks.xls.gz |
1.2 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
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