Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
STAT3

Cell type

Cell type Class
Breast
Cell type
HCC70
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
HCC70 Cell Line
chip antibody
sc-482
treatment
EtOH
cell line
HCC70

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP experiments, protein-DNA complexes were covalently cross-linked by incubating cells in 1% formaldehyde for 10 min at room temperature. Cells were incubated with 0.125 M glycine for 5 min, to quench cross-linking reaction. Cells were washed and scraped with PBS (pH 7.4) (Lonza). Cells were lysed with Farnham Lysis Buffer (5mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) containing protease inhibitor (Roche). Cell lysate was centrifuged at 2,000 rpm for 5 min at 4 °C. The crude nuclear extract contained in the supernatant was stored at −80 °C. ChIP-seq libraries were constructed as described here: https://www.encodeproject.org/documents/df9dd0ec-c1cf-4391-a745-a933ab1af7a7/@@download/attachment/Myers_Lab_ChIP-seq_Protocol_v042211.pdf

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
17123261
Reads aligned (%)
88.8
Duplicates removed (%)
6.2
Number of peaks
13660 (qval < 1E-05)

hg38

Number of total reads
17123261
Reads aligned (%)
90.5
Duplicates removed (%)
5.2
Number of peaks
13723 (qval < 1E-05)

Base call quality data from DBCLS SRA