Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231
cell line
MDA-MB-231
cell type
human breast cell line
immunoprecipitation
ab28379, abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of 15µl of anti-SOX4 (CS-129-100, Diagenode) or 2µg of anti-SMAD3 (ab28379, abcam) coupled to A/G sepharose beads (Santa Cruz Biotechnology). Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
24334497
Reads aligned (%)
64.7
Duplicates removed (%)
9.0
Number of peaks
57996 (qval < 1E-05)

hg19

Number of total reads
24334497
Reads aligned (%)
64.6
Duplicates removed (%)
9.1
Number of peaks
58023 (qval < 1E-05)

Base call quality data from DBCLS SRA