Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF-7 Cell Line
chip antibody
sc-1003
treatment
100nM dexamethasone
cell line
MCF-7

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
26835020
Reads aligned (%)
87.1
Duplicates removed (%)
7.5
Number of peaks
14017 (qval < 1E-05)

hg38

Number of total reads
26835020
Reads aligned (%)
88.9
Duplicates removed (%)
6.4
Number of peaks
13886 (qval < 1E-05)

Base call quality data from DBCLS SRA