Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

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 cells
cell line
MDA-MB-231
cancer
Breast adenocarcinoma
chip antibody
Glucocorticoid Receptor (D8H2) XP® Rabbit mAb #3660 from CST

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody. For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
202660273
Reads aligned (%)
113.9
Duplicates removed (%)
34.5
Number of peaks
1598 (qval < 1E-05)

hg38

Number of total reads
202660273
Reads aligned (%)
116.4
Duplicates removed (%)
33.6
Number of peaks
2682 (qval < 1E-05)

Base call quality data from DBCLS SRA