Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

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
Breast cancer cell line
cell-type
MCF7
chip antibody
aGATA3 (sc-268, Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect TRPS1 (10ug, sc-26974, Santa Cruz; 5ug, AF4838, R&D) and GATA3 (10ug, sc-268, Santa Cruz) with 100 ml Protein A or G magnetic beads (Thermo Scientific). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
40198606
Reads aligned (%)
74.4
Duplicates removed (%)
15.1
Number of peaks
26688 (qval < 1E-05)

hg38

Number of total reads
40198606
Reads aligned (%)
76.0
Duplicates removed (%)
14.0
Number of peaks
26151 (qval < 1E-05)

Base call quality data from DBCLS SRA