Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Breast
Cell type
SUM 159PT
Primary Tissue
Breast
Tissue Diagnosis
Anaplastic Carcinoma

Attributes by original data submitter

Sample

source_name
SUM159 Cell Line
chip antibody
sc-1003
treatment
100nM dexamethasone
cell line
SUM159

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
17680931
Reads aligned (%)
87.7
Duplicates removed (%)
8.1
Number of peaks
40824 (qval < 1E-05)

hg38

Number of total reads
17680931
Reads aligned (%)
88.8
Duplicates removed (%)
7.5
Number of peaks
39919 (qval < 1E-05)

Base call quality data from DBCLS SRA