|
| Status |
Public on May 23, 2023 |
| Title |
PHF8-sgRNA c-MYC |
| Sample type |
SRA |
| |
|
| Source name |
786-O
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-O
cell type: clear cell renal cell carcinoma
transfection: sgRNA targeting PHF8
chip antibody: c-MYC (CST, #9402)
|
| Treatment protocol |
c-MYC ChIP-seq in 786-O cells transfected with Ctrl-sgRNA (normal control, NC) and PHF8-sgRNA; PHF8 ChIP-seq in 786-O cells transfected with siRNA targeting c-MYC and scrambled siRNA as control.
|
| Growth protocol |
RPMI 1640, 10% fetal bovine serum, Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 125 mM glycine.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4)
Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality
The clean reads were mapped to the human genome (assembly human genome GRCh38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software
Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff
Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10)
Assembly: hg38
Supplementary files format and content: bw
|
| |
|
| Submission date |
May 22, 2023 |
| Last update date |
May 23, 2023 |
| Contact name |
Jun Jiang |
| E-mail(s) |
jiangjun_64@yahoo.com
|
| Organization name |
Daping Hospital, Army Medical University
|
| Department |
Department of Urology
|
| Lab |
Institute of Surgery Research
|
| Street address |
10#, Changjiang Zhilu, Yuzhong District
|
| City |
Chongqing |
| State/province |
Chongqing |
| ZIP/Postal code |
400042 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE217161 |
ChIP-seq of PHF8 and c-MYC in 786-O cell line |
|
| Relations |
| BioSample |
SAMN35309294 |
| SRA |
SRX20465964 |
