Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Colorectal
cell line
HCT116
genotype
QSER1 SH-1
chip antibody
P53(Santa Cruz sc-126)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed according to the previously published protocol (Guo et al.,2020). Briefly, HCT-116 cells were crosslinked with 1% formaldehyde (sigma) for 10 min and quenched with glycine (sangon biotech) for 5 min at the room temperature. Fixed cells were sonicated and immunoprecipitated with the mixture of ProteinA Agarose (ROCHE) and antibody overnight at 4 ℃. ChIP-DNA was purified using PCR purification kit (Qiagen) and performed for qPCR using iTaq™ Universal SYBR® Green Supermix (Bio-Rad) on CFX96 (Bio-Rad). The ChIP-seq sample preparation kit was used to prepare generate ChIP-seq library. NEBNext® DNA Library Prep Master Mix Set for Illumina

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg38

Number of total reads
19811598
Reads aligned (%)
89.6
Duplicates removed (%)
14.9
Number of peaks
1497 (qval < 1E-05)

hg19

Number of total reads
19811598
Reads aligned (%)
88.9
Duplicates removed (%)
15.2
Number of peaks
1254 (qval < 1E-05)

Base call quality data from DBCLS SRA