Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA2

Cell type

Cell type Class
Uterus
Cell type
Endometrial stromal cells
NA
NA

Attributes by original data submitter

Sample

source_name
Endometrial biopsy from healthy women
gender
female
cell type
Primary endometrial stromal cells
passage
3-5
chip antibody
GATA2 (Santa Cruz Biotechnologies, sc-9008)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed for 15 min with 1/10 volume of freshly prepared formaldehyde solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, and 50 mM HEPES). The fixation was stopped by adding 1/20 volume 2.5 M glycine for 5 min. Fixed HESCs were collected and pelleted at 800 x g for 10 min at 4 oC. Cell pellets were washed two times with cold PBS-Igepal (0.5% Igepal, 1 mM PMSF). HESCs from six patients were pooled before genomic DNA isolation. NR2F2 immunoprecipitation and DNA library generation were performed by Active Motif. ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit. Briefly, DNA ends were polished and 59-phosphorylated using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. Addition of 3'-adenine to blunt ends using Klenow fragment (3'-5' exo minus), Illumina genomic adapters were ligated and the sample was size fractionated to 175–225 bp on a 2% agarose gel. After amplification for 18 cycles with Phusion polymerase, the resulting DNA libraries were tested by RT-qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
40515129
Reads aligned (%)
58.6
Duplicates removed (%)
40.0
Number of peaks
58877 (qval < 1E-05)

hg38

Number of total reads
40515129
Reads aligned (%)
59.3
Duplicates removed (%)
39.5
Number of peaks
58971 (qval < 1E-05)

Base call quality data from DBCLS SRA