Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Uterus
Cell type
Endometrial Stromal Tumors
MeSH Description
Neoplasms of the endometrial stroma that sometimes involve the MYOMETRIUM. These tumors contain cells that may closely or remotely resemble the normal stromal cells. Endometrial stromal neoplasms are divided into three categories: (1) benign stromal nodules; (2) low-grade stromal sarcoma, or endolymphatic stromal myosis; and (3) malignant endometrial stromal sarcoma (SARCOMA, ENDOMETRIAL STROMAL).

Attributes by original data submitter

Sample

source_name
Tamoxifen-associated endometrial tumor
tissue
endometrioid adenocarcinoma
chip antibody
FOXA1/2 (SC-6554; Santa cruz)

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), FOXA1/2 (SC-6554; Santa Cruz), RNA Pol II (ab5408; abcam) and H3K27ac (39133; Active Motif), which were coupled to Dynabeads prot A, prot G, prot G and prot A, respectively. 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
15259727
Reads aligned (%)
88.6
Duplicates removed (%)
3.8
Number of peaks
2177 (qval < 1E-05)

hg38

Number of total reads
15259727
Reads aligned (%)
90.8
Duplicates removed (%)
2.4
Number of peaks
2121 (qval < 1E-05)

Base call quality data from DBCLS SRA