Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU5F1

Cell type

Cell type Class
Epidermis
Cell type
Dermal fibroblast
NA
NA

Attributes by original data submitter

Sample

source_name
Foreskin fibroblasts
tissue
Foreskin fibroblasts
cell line
A2B5+ iOPCs(H)
chip antibody
OCT4(OCT3/4)
chip antibody vendor
Santa Cruz Biotechnology

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
H9-hESCs and A2B5+ iOPCs were cross-linked with 1% (wt/vol) formaldehyde fixation buffer, resuspended and lysed using an EZ-ChIP kit (Upstate, Millipore). To shear the cross-linked DNA, the lysates were subjected to 30 cycles of 30 seconds of sonication followed by 30 seconds of rest on ice with a Bioruptor sonicator (Diagenode, UCD-200) and incubated with protein G agarose beads and 3 μg of an anti-OCT4 antibody overnight at 4°C. After chromatin immunoprecipitation, the rest of the experiments were performed according to the manufacturer's protocols The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
36833489
Reads aligned (%)
8.9
Duplicates removed (%)
89.3
Number of peaks
385 (qval < 1E-05)

hg38

Number of total reads
36833489
Reads aligned (%)
10.4
Duplicates removed (%)
87.5
Number of peaks
398 (qval < 1E-05)

Base call quality data from DBCLS SRA