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
HCT116
cell line
HCT116
treated with
4GY for 2hrs
chip antibody
anti-p53 antibody (DO-1, Santa Cruz Biotechnology, SC-126X, Lot:G0115)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPseq lysates were clarified from sonicated nuclei and IPed with DO-1 anti-p53 antibody. RNA samples were extracted with Trizol, purified on Zymo columns, and 500ng polyA selected. DNA and mRNA libraries were prepared with standard illumina compatible protocols (NEBnext Kit), ATACseq Lib was prepared by PCR of MuA tagmented DNA.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
19298946
Reads aligned (%)
72.5
Duplicates removed (%)
19.0
Number of peaks
925 (qval < 1E-05)

hg38

Number of total reads
19298946
Reads aligned (%)
73.6
Duplicates removed (%)
18.2
Number of peaks
835 (qval < 1E-05)

Base call quality data from DBCLS SRA