|
| Status |
Public on Feb 28, 2021 |
| Title |
phGC_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Hy-Line Brown
tissue: follicle
cell type: granulosa
development stage: pre-hierarchical
age: 35-40 week
chip antibody: H3K27ac (Abcam, ab4729)
|
| Growth protocol |
The primary granulosa cells were pre-cultured with Medium 199 (Gibco, USA) and 5% FBS (Gibco, USA) overnight (8h).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin was obtained by cell lysis (50 mM HEPES, pH 7.5; 150 mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; and proteinase inhibitors) and was followed by sonication (Sonics VCX130, USA) on ice for 6 min. DNA (1 μg) was used for the preparation of the Chromatin Immunoprecipitation Sequencing (ChIP-Seq) library by NEBNext UltraII DNA Library Prep Kit for Illumina (NEB, USA, E7645 and E7335), according to the manufacturer’s instructions. The ChIP DNA library was sent to Novogene Co., Ltd. (Beijing, China) for paired-end 150 bp sequencing on the Illumina Nova platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were filtered by removing adapters, low quality reads and unknown bases
Clean reads were mapped to Gallus_gallus-5.0 of ensembl using Bowtie2 v2.3.4.1
MACS2 (v2.1.1.20160309) was used for peak calling with parameters -B -p 1e-9, where chicken genome size is set to 1.2e9
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: bedGraph files were generated using MACS2
|
| |
|
| Submission date |
Dec 27, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Ying Huang |
| E-mail(s) |
ying.huang@webmail.hzau.edu.cn
|
| Organization name |
Huazhong Agricutural University
|
| Street address |
No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26853 |
| Series (2) |
| GSE163889 |
Comparative analysis among different species reveals that androgen receptor is a core transcriptional factor regulating the chicken follicular selection and ovulation [ChIP-Seq] |
| GSE163891 |
Comparative analysis among different species reveals that the androgen receptor regulates chicken follicle selection through species-specific genes related to follicle development |
|
| Relations |
| BioSample |
SAMN17168606 |
| SRA |
SRX9738702 |
