Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX2

Cell type

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

Attributes by original data submitter

Sample

source_name
H9_SOX2_AF2018
cell lines
H9
antibody
SOX2
antibody vendor
R&D (AF2018)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified and subjected to standard Illumina library construction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
12000000
Reads aligned (%)
91.2
Duplicates removed (%)
4.2
Number of peaks
1024 (qval < 1E-05)

hg38

Number of total reads
12000000
Reads aligned (%)
93.4
Duplicates removed (%)
2.7
Number of peaks
823 (qval < 1E-05)

Base call quality data from DBCLS SRA