|
| Status |
Public on Jul 01, 2024 |
| Title |
Chicken preadipocytes - TCF21_IP_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Chicken preadipocyte stably overexpressing TCF21 (LV-TCF21)
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: Adipose derived-chicken preadipocyte stably overexpressing TCF21 (LV-TCF21)
chip antibody: anti-HA antibody, Abcam, ab9110
treatment: Treatment with oleic acid for 24h
|
| Treatment protocol |
At 50% confluency of the plated cells, differentiation was induced by replacing fresh differentiation media (DMEM with 10% FBS and 300 μM oleic acid) for 24h.
|
| Growth protocol |
The preadipocytes were initially grown in DMEM (Gibco, NY, USA) with 10% FBS (Biological Industries) in a standard humidified incubator. At >90% confluency, the cells were either passaged or plated for follow-up experiments at 1×105 cells/ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were then collected, treated with nuclear lysis buffer, and sonicated to mediate DNA fragmentation. The sonicated chromatin was used in each immunoprecipitation reactions with the anti-HA antibody (Abcam) or with control rabbit IgG (Cell Signaling Technology).
Libraries were prepared according to Illumina's instructions. The brief procedures are end repair, adding 3' A tail, ligating adaptors and enriching/linearizing with PCR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of chicken (Gallus_gallus-5.0) using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling.
The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test. The Homer（version 4.10）was used for motifs analysis.
Genome_build: Gallus_gallus-5.0
|
| |
|
| Submission date |
Jul 01, 2021 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Xinyang Zhang |
| E-mail(s) |
xinyanglucy@sina.com
|
| Phone |
+8618846791714
|
| Organization name |
Northeast Agricultural University
|
| Department |
Animal Science and Technology
|
| Lab |
Key Laboratory of Chicken Genetics and Breeding
|
| Street address |
No.600 Changjiang street
|
| City |
Harbin |
| State/province |
Heilongjiang |
| ZIP/Postal code |
150030 |
| Country |
China |
| |
|
| Platform ID |
GPL24517 |
| Series (1) |
| GSE179259 |
Genome-wide binding sites of transcription factor 21 in chicken preadipocytes |
|
| Relations |
| BioSample |
SAMN19987837 |
| SRA |
SRX11326538 |
