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
cell type
hESC
chip antibody
SOX2 (R&D 2018)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and SOX2-DNA complexes and POI II-DNA complexes were immunoprecipitated with SOX2 antibody (R&D AF2018) or POI II antibody (Covance MMS-126R). Protein A and G Magenetic Dynabeads were used to capture antibody bound protein-DNA complexes. ChIP-seq libraries preparation: The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding ‘‘A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq2500 platforms.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
40948719
Reads aligned (%)
85.7
Duplicates removed (%)
4.1
Number of peaks
17313 (qval < 1E-05)

hg38

Number of total reads
40948719
Reads aligned (%)
87.6
Duplicates removed (%)
2.9
Number of peaks
16947 (qval < 1E-05)

Base call quality data from DBCLS SRA