|
| Status |
Public on May 07, 2021 |
| Title |
Vec_PHF8_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
RKO cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: vector
cell line: RKO cell line
chip antibody: PHF8 (abcam, ab36068, lot: GR3195675-1)
|
| Treatment protocol |
RKO cells were transfected with vector or APOC2 overexpression plasmid.
|
| Growth protocol |
RKO cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using the ChIP-IT High Sensitivity (HS) Kit (Active Motif 53040) according to the manufacturer’s recommended protocol.
ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina HiSeq Xten platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
All ChIP-seq reads were aligned to the hg38 reference human genome by Bowtie 2 (version 2.2.9)
Enriched PHF8 occupancies were called using MACS (version 2.0) with default settings. And the -B --trackline settings were used for generating the bedGraph files.
The enriched regions were annotated using the annotatePeaks package from the HOMER suite
Supplementary_files_format_and_content: bedGraph, peaks bed
|
| |
|
| Submission date |
May 07, 2018 |
| Last update date |
May 07, 2021 |
| Contact name |
Jian Chen |
| E-mail(s) |
yufuchenjian@163.com
|
| Organization name |
Shanghai pulmonary Hospital
|
| Department |
Department of thoracic Surgery
|
| Street address |
507 Zhengmin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE114089 |
APOC2 increase PHF8 binding on chromatin |
|
| Relations |
| BioSample |
SAMN09080689 |
| SRA |
SRX4047133 |
