Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Lung
Cell type
Calu-1
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Cell Line
cell line
Calu-1
genotype/variation
p53 R158G mutant
treatment
DMSO
chip antibody
p53 (#9282, Cell Signaling)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
In brief, cells were crosslinked with 1% formaldehyde, glycine quenched, lysed with cell lysis buffer (Sigma, #2978) supplemented with 1 mM PMSF, and subjected to pulse sonication (20s with 30s internal, 5 cycles). The supernatant was then immunoprecipitated with the p53 and rabbit IgG antibodies (Cell Signaling, #9282 and #2729) at 4°C overnight and incubated with Magna ChIP Protein G magnetic beads (Millipore, #16-662). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
4107550
Reads aligned (%)
124.9
Duplicates removed (%)
21.9
Number of peaks
211 (qval < 1E-05)

hg38

Number of total reads
4107550
Reads aligned (%)
130.1
Duplicates removed (%)
20.9
Number of peaks
384 (qval < 1E-05)

Base call quality data from DBCLS SRA