Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP53

Cell type

Cell type Class
Breast
Cell type
Breast cancer cells
NA
NA

Attributes by original data submitter

Sample

source_name
triple negative breast cancer
cell type
tumor-derived cancer cells
passages
10 to 20
chip antibody
sc-126, Santa Cruz

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells on six 15 cm plates of MDA-MB-231 per IP were fixed with 1% formaldehyde for 20 min., washed with PBS, scraped and lysed in Lysis Buffer - 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, nuclei spun down, washed in 10 mM Tris-HCl, pH 7.5, 200 mM NaCl, 1mM EDTA and resuspended in Sheraing Buffer - 0.1% SDS, 1mM EDTA, 10 mM Tris, pH 7.5. Samples were sonicated using Bioruptor sonicator (Diagenode) for the total time of 30 min., to achieve average size of 250-300 bp of the sonicated chromatin fragments. The Shearing Buffer was then supplemented to RIPA buffer and the rest of the protocol followed as described in Girardini et al, Cancer Cell, 2011. 2–10 ng DNA resulting form the ChIP procedure was prepared for HiSeq2000 sequencing with TruSeq ChIP Sample Prep Kit (Illumina) following the manufacturer’s instructions 50 base pair single reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
23411048
Reads aligned (%)
90.1
Duplicates removed (%)
4.4
Number of peaks
856 (qval < 1E-05)

hg38

Number of total reads
23411048
Reads aligned (%)
92.3
Duplicates removed (%)
3.0
Number of peaks
713 (qval < 1E-05)

Base call quality data from DBCLS SRA