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
p53 ChIP-seq
cell line
HCT116
cell type
colorectal cancer cell
antibody
p53-specific DO1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP and Input DNA libraries for single end sequencing were prepared with the Illumina ChIP-Seq DNA Sample Prep kit according to the manufacturer’s instructions. DNA was purified using QIAGEN PCR clean up kit, DNA fragments were 3’ A-tailed and ligated to Illumina adapters. Adapter-ligated DNA was purified using Agencourt AMPure kit, and the entire amount of eluted DNA was used for PCR amplification (10-12 cycles). The PCR amplified ChIP and Input libraries were subjected to electrophoresis and fragments with average size ~200-400 bp were recovered using the QIAGEN gel extraction kit. Libraries was quantified on Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit and single end sequencing was performed on Illumina Genome Analyzer 2x.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
13769858
Reads aligned (%)
87.7
Duplicates removed (%)
6.5
Number of peaks
444 (qval < 1E-05)

hg38

Number of total reads
13769858
Reads aligned (%)
89.1
Duplicates removed (%)
5.9
Number of peaks
206 (qval < 1E-05)

Base call quality data from DBCLS SRA