Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

Cell type Class
Blood
Cell type
Pre-B lymphoblast cells
NA
NA

Attributes by original data submitter

Sample

source_name
Pre-B lymphoblast cells
cell type
Blast from BCP-ALL patient
tissue
Bone marrow
disease state
Human BCP-ALL
chip antibody
RUNX1 (ab23980, Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% formaldehyde (648336, Polysciences) at room temperature for 10 min and then quenched in 100 mM glycine for 1 min. Cells were washed twice in PBS and lysed 15 min in 50 mM Tris-HCl ph8.1/10 mM EDTA/0.5% Empigen BB/1% SDS. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIP-seq libraries were generated using TruSeq® ChIP Library Preparation Kit (Illumina) according to the manufacturer's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 1500

hg19

Number of total reads
22115758
Reads aligned (%)
89.2
Duplicates removed (%)
5.3
Number of peaks
29694 (qval < 1E-05)

hg38

Number of total reads
22115758
Reads aligned (%)
90.2
Duplicates removed (%)
4.8
Number of peaks
29752 (qval < 1E-05)

Base call quality data from DBCLS SRA