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 derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
H9 derived NPCs
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
40469539
Reads aligned (%)
84.8
Duplicates removed (%)
6.7
Number of peaks
50265 (qval < 1E-05)

hg38

Number of total reads
40469539
Reads aligned (%)
86.4
Duplicates removed (%)
5.7
Number of peaks
50354 (qval < 1E-05)

Base call quality data from DBCLS SRA