Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

Cell type

Cell type Class
Uterus
Cell type
Carcinoma, Endometrioid
MeSH Description
An adenocarcinoma characterized by the presence of cells resembling the glandular cells of the ENDOMETRIUM. It is a common histological type of ovarian CARCINOMA and ENDOMETRIAL CARCINOMA. There is a high frequency of co-occurrence of this form of adenocarcinoma in both tissues.

Attributes by original data submitter

Sample

source_name
Endometrial tumor of a non-tamoxifen-user 3
tissue
endometrioid adenocarcinoma
chip antibody
ERa (SC-543; Santa Cruz)
procedure
Chromatin IP against ERa

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fresh Frozen tumor was crosslinked with 1% formaldehyde for 20 minutes, quenched with 2 M Glycin for 5 minutes, and washed twice with PBS. Nuclei were isolated and sonicated. ChIP was performed with ERa (sc-543; Santa Cruz), and H3K27ac (39133; Active Motif), which were coupled to Dynabeads prot A. Samples were washed with RIPA buffer and reverse crosslinked at 65 C O/N. Samples were treated with RNAse A and prot K and DNA was isolated by alcohol precipitation. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
30403020
Reads aligned (%)
55.4
Duplicates removed (%)
9.6
Number of peaks
5506 (qval < 1E-05)

hg38

Number of total reads
30403020
Reads aligned (%)
57.1
Duplicates removed (%)
7.8
Number of peaks
5506 (qval < 1E-05)

Base call quality data from DBCLS SRA