|
| Status |
Public on May 01, 2020 |
| Title |
Input-2-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT116
treatment: None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Input for DMSO-p53-SC-rep2, 5FU-p53-SC-rep2 and Nutlin3a-p53-SC-rep2
|
| Data processing |
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.
|
| |
|
| Submission date |
Jan 30, 2019 |
| Last update date |
May 01, 2020 |
| Contact name |
Qinglan Li |
| E-mail(s) |
liqinglan@whu.edu.cn
|
| Organization name |
Wuhan University
|
| Street address |
Room 5005, Life Science College, Wuhan University
|
| City |
Wuhan City |
| State/province |
Hubei Province |
| ZIP/Postal code |
430062 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE125927 |
Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes [ChIP-seq] |
| GSE125928 |
Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes |
|
| Relations |
| BioSample |
SAMN10848895 |
| SRA |
SRX5313214 |
