Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NANOG

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA

Attributes by original data submitter

Sample

source_name
H9 hESC
cell line
H9 ESC
chip antibody
Anti-Nanog antibody (R&D AF1997)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Anti-Nanog antibody (R&D AF1997) was used. Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7370L)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24792520
Reads aligned (%)
121.6
Duplicates removed (%)
30.2
Number of peaks
5160 (qval < 1E-05)

hg38

Number of total reads
24792520
Reads aligned (%)
123.0
Duplicates removed (%)
30.0
Number of peaks
5266 (qval < 1E-05)

Base call quality data from DBCLS SRA