Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

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

Attributes by original data submitter

Sample

source_name
hESC H9 cell line
target
RUNX1
cell line
H9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed on CD34+ magnetic sorted samples (RUNX1-ETO and RUNX) and on non-adhered floating mixed progenitors (H3K4me3 and H3K27ac) after single crosslink. Antibodies were used against the following antigens (manufacturer, cat #): HA tag (Sigma, H6908), RUNX1 (ab23980, Abcam), H3K27ac (Abcam, ab4729), H3K4me3 (Merk, 07-473), H3K79me2 (Abcam, ab3594). For H3K79me2 ChIP, a concentration of at least 0.2% SDS on the chromatin suspension was used and immunoprecipitation was carried overnight. ChIP libraries for Illumina sequencing were prepared using the KAPA Hyper Prep Kit (Roche, KR0961), as detailed by the manufacturer. Quality control of the libraries was performed using a High Sensitivity DNA chip on an Agilent Technologies 2100 Bioanalyser instrument and libraries were quantified using the RT-qPCR-based method KAPA Library Quantification Kit for Illumina Sequencing Platforms, following the manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
47284011
Reads aligned (%)
86.4
Duplicates removed (%)
10.8
Number of peaks
6164 (qval < 1E-05)

hg38

Number of total reads
47284011
Reads aligned (%)
89.1
Duplicates removed (%)
8.8
Number of peaks
6444 (qval < 1E-05)

Base call quality data from DBCLS SRA