Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

Cell type

Cell type Class
Uterus
Cell type
Ishikawa
Primary Tissue
Uterus
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Ishikawa (Endometrioid adenocarcinoma)
cell line
Ishikawa
enhancer deleted
MMP17-2
treatment
10nM E2 1hr
antibody target
Estrogen Receptor alpha

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To crosslink chromatin, 37% formaldehyde (Sigma-Aldrich) was added directly to the media and allowed to incubate at room temperature for 10 minutes. Glycine was added at a final concentration of 125 mM to stop crosslinking, and cells were washed with cold 1X PBS. Plates were scraped in Farnham lysis buffer with 1X protease inhibitor (Thermo Fisher). Chromatin was sonicated using an Active Motif EpiShear Probe Sonicator with 6 cycles of 30 s, at 40% amplitude, with 30 s of rest. ChIP was performed as previously described (Reddy et al., 2009) using anti-ER (Santa Cruz HC-20) and anti-H3K27ac (Active Motif 39133) antibodies. ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009. The following antibodies were used: H3K27ac (Active Motif pAb Cat #39133) and ER (Santa Cruz HC-20) Libraries were sequenced on an Illumina HiSeq 2500 as single-end 50 basepair reads

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
13477208
Reads aligned (%)
68.8
Duplicates removed (%)
17.3
Number of peaks
14094 (qval < 1E-05)

hg38

Number of total reads
13477208
Reads aligned (%)
69.6
Duplicates removed (%)
16.9
Number of peaks
14034 (qval < 1E-05)

Base call quality data from DBCLS SRA