Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAT3

Cell type

Cell type Class
Breast
Cell type
MCF 10A
Primary Tissue
Breast
Tissue Diagnosis
Fibrocystic Disease

Attributes by original data submitter

Sample

source_name
MCF10A-ER-Src cell
tissue
Breast
cell line
MCF10A-ER-Src
chip target
STAT3
transformation status
non-transformed

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP experiments follow the ENCODE protocol, http://genome.ucsc.edu/ENCODE/, using the following antibodies: STAT3 (Cell Signaling, 9131), NFKB1 (Sigma, HPA027305), FOS (Santa Cruz Biotech, SC-7202x), JUN (Santa Cruz Biotech, SC-1694) and JUNB (Santa Cruz Biotech, SC-73). We performed the ChIP experiments, using the non-transformed MCF10A-ER-Src cells and the cells after 12hr of cell transformation. Library preparation and sequencing were carried out as per ENCODE protocols, and a detailed protocol is available at http://genome.ucsc.edu/ENCODE/

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
28526639
Reads aligned (%)
52.8
Duplicates removed (%)
43.9
Number of peaks
9357 (qval < 1E-05)

hg38

Number of total reads
28526639
Reads aligned (%)
54.5
Duplicates removed (%)
42.6
Number of peaks
9384 (qval < 1E-05)

Base call quality data from DBCLS SRA