Antigen

Antigen Class

TFs and others

Antigen

SOX2

Cell type

Cell type Class

Pluripotent stem cell

Cell type

hESC derived neural cells

NA

NA

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

hg38

Number of total reads

40469539

Reads aligned (%)

91.6

Duplicates removed (%)

5.7

Number of peaks

50354 (qval < 1E-05)

hg19

Number of total reads

40469539

Reads aligned (%)

90.8

Duplicates removed (%)

6.7

Number of peaks

50265 (qval < 1E-05)