Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR3C1

Cell type

Cell type Class
Breast
Cell type
Breast cancer
NA
NA

Attributes by original data submitter

Sample

source_name
Human breast tumor
antibody
GR
patient id
Male_21
tissue
Human breast tumor
Sex
male

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Tissue was defrosted and crosslinked in solution A (50 mM Hepes, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, pH= 7.4) containing 2 mM DSG, incubated for 25 minutes at room temperature while rotating. After 25 minutes formaldehyde was added to 1% final and incubated another 20 minutes at room temperature with rotation. Samples were quenched by adding a surplus of 0.2M glycine, pelleted by centrifugation (5'@4000rcf 4°C), washed with cold PBS and mechanically disrupted in cold PBS using a pellet pestle (Sigma). The PicoBioruptor (Diagenode) was used for sonication. For ChIP, antibodies were used to detect ERα (sc-543, Santa Cruz), AR (sc-816, Santa Cruz), FOXA1 (sc-6554, Santa Cruz), PR (sc-7208, Santa Cruz), GR (12041S lot 3, Cell Signaling Technology) and H3K4me1 (ab8895, AbCam). Immunoprecipitated DNA was prepared for Illumina multiplex-sequencing with 10 samples per lane at 65bp single end. For steroid hormone receptor ChIPs, 5µg of antibody and 50µl dynabeads (Invitrogen) were used, for FOXA1 and H3K4me1, 4µg of antibody and 40µl magnetic beads were used. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
25669656
Reads aligned (%)
80.0
Duplicates removed (%)
3.8
Number of peaks
4088 (qval < 1E-05)

hg38

Number of total reads
25669656
Reads aligned (%)
81.0
Duplicates removed (%)
3.1
Number of peaks
4053 (qval < 1E-05)

Base call quality data from DBCLS SRA