|
Status |
Public on May 01, 2020 |
Title |
siGLIS2.2-DMSO-p53-Input |
Sample type |
SRA |
|
|
Source name |
Colorectal cancer cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: HCT116 treatment: DMSO
|
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).
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|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
HiSeq X Ten |
|
|
Description |
Input for siGLIS2.2-DMSO-p53
|
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.
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|
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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 |
SAMN10848882 |
SRA |
SRX5313224 |