Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU5F1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
Induced pluripotent stem cells
cell type
Induced pluripotent stem cells
chip antibody
anti OCT3 antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatins were fragmentated by sonication and immunoprecipitated with an anti-FLAG M2 antibody or antibodies against protein-of-interest. Immunoprecipitated DNA fragments were purified by QIAGEN's PCR purification Kit. Ten ng of co-immunoprecipitated DNA fragments, exept for Of-S-M and O-Sf-M, were subjected to preparation of Illumina’s sequencing library using NEBNext ChIP-seq Library Prep Reagent (New England Biolabs), according manifacturer's instruction. After adapter ligation, DNA fragments were amplified by PCR with Illumina primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated by Caliper XT(Perkinelmer). For Of-S-M and O-Sf-M, Illumina’s sequencing libraries were generated by Ovation SP Iltralow Library System (NuGEN). The purified DNA was captured on an Illumina flow cell for cluster generation.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
43570306
Reads aligned (%)
60.6
Duplicates removed (%)
20.2
Number of peaks
7344 (qval < 1E-05)

hg38

Number of total reads
43570306
Reads aligned (%)
62.0
Duplicates removed (%)
19.1
Number of peaks
7535 (qval < 1E-05)

Base call quality data from DBCLS SRA