Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480 Cells
cell line
SW480
cell type
Colon Cancer Cells
genotype/variation
Human Colon Cancer Cell Line, stable p53 knockdown
treatment
TNF-a
chip antibody
anti-p53 (FL393, sc6243)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, cells were crosslinked, lysates from sonicated nuclei were prepared, and protein-DNA complexes were immunoprecipitated with corresponding antibodies. Please refer to the methods section for detailed protocols. ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. Briefly, ChIP DNA was end-repaired and adaptors were ligated to the ends of the DNA fragments. Adaptor-ligated ChIP DNA fragments with average size of 350 bp were used to construct libraries and single-end sequenced on Illumina HiSeq 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
58251154
Reads aligned (%)
72.2
Duplicates removed (%)
14.1
Number of peaks
11606 (qval < 1E-05)

hg38

Number of total reads
58251154
Reads aligned (%)
73.4
Duplicates removed (%)
13.3
Number of peaks
11632 (qval < 1E-05)

Base call quality data from DBCLS SRA