Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H1
NA
NA

Attributes by original data submitter

Sample

source_name
H1hESC_ChIP_GATA3_6h
cell line
H1
cell type
human embryonic stem cells (hESCs)
treatment
BMP4
treatment_duration_hrs
6
repeat
2
chip antibody
GATA3 (Abcam; ab199428)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were dissociated and fixed in mTeSR1 media with formaldehyde at a final concentration of 1% for 10 minutes. Fixation was quenched with glycine and cells were washed with DPBS. Cells were suspended in high salt lysis buffer and chromatin was sheared using a Bioruptor Plus to sizes of 100-400 bp. Soluble chromatin from approximately 3E+06 cells per ChIP was incubated with primary antibody (Abcam; ab199428) and Protein G Dynabeads at 4 degrees overnight. Dynabeads were then washed and bound chromatin was eluted. Crosslinks were reversed by incubation at 65 degrees overnight, and proteins were digested with Proteinase K. DNA was purified using Zymo ChIP Clean and Concentrator Kit. Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
40606232
Reads aligned (%)
80.9
Duplicates removed (%)
13.3
Number of peaks
8193 (qval < 1E-05)

hg38

Number of total reads
40606232
Reads aligned (%)
82.4
Duplicates removed (%)
12.3
Number of peaks
8394 (qval < 1E-05)

Base call quality data from DBCLS SRA