Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NR5A1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
CHIR-treated NR5A1-DOX (+) cells
cell type
Human embryonic stem cells (H9)
culture condition
CHIR condition
genotype
NR5A1 overexpression

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was prepared from 10 million crosslinked cells for immunoprecipitation. The samples were sheared in a Covaris S220 Focused-ultrasonicator and then reacted with 10 µg rabbit anti-H3K4me3 (ab8580; Abcam) and rabbit anti-H3K27me3 (07-449; Merck Millipore) antibodies, and Normal Rabbit IgG (CST) for Histone-ChIP, and with 10 µg mouse anti-DDDDK-tag (FLA-1, MBL) and Normal Mouse IgG (Santa Cruz Biotechnology for NR5A1-ChIP. Total inputs and ChIPed samples were evaluated using an Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit for library preparation. Libraries for Miseq sequencing were prepared using a TruSeq DNA Sample Preparation Kit (Illumina) according to a manufacturer’s instructions. After adopter ligation, DNA fragments of 300–400 bp were excised from 2% agarose gels. The purified DNA was amplified by 15–18 cycles of PCR. The libraries were evaluated using an Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit. The validated libraries were loaded into Miseq Reagent Kit v3 (150 cycles) at a final concentration of 10 pM. Sequencing was performed in a Miseq sequencer (Illumina) using the paired end mode.

Sequencing Platform

instrument_model
Illumina MiSeq

hg19

Number of total reads
14799127
Reads aligned (%)
188.3
Duplicates removed (%)
4.2
Number of peaks
24929 (qval < 1E-05)

hg38

Number of total reads
14799127
Reads aligned (%)
190.6
Duplicates removed (%)
3.8
Number of peaks
25218 (qval < 1E-05)

Base call quality data from DBCLS SRA