Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HDAC2

Cell type

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

Attributes by original data submitter

Sample

source_name
hESCs
cell type
human embryonic stem cells (hESCs)
passages
p55
reprogramming method
None
clone
None
chip antibody
HDAC2 (Cell Signaling, 2545S)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
12257584
Reads aligned (%)
111.9
Duplicates removed (%)
42.5
Number of peaks
134 (qval < 1E-05)

hg38

Number of total reads
12257584
Reads aligned (%)
112.5
Duplicates removed (%)
42.4
Number of peaks
197 (qval < 1E-05)

Base call quality data from DBCLS SRA