Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX2

Cell type

Cell type Class
Blood
Cell type
KARPAS-45
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
KARPAS-45
cell type
T-ALL cell line
cell line
KARPAS-45
chip antibody
RUNX2 (D1H7, Cell Signalling Technology)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
107 cells were cross-linked for each ChIP experiment with 1.1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. The purified chromatin was fragmented to 200–300 bp fragments by sonication (Covaris, Woburn, MA, USA; S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 μl of protein-A coated beads (Thermo-Scientific, Waltham, MA, USA; catalog number 53139) and 10 μg of the specified antibodies. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65 °C overnight. DNA was subsequently purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime DNA obtained from the ChIP assays was adaptor ligated, amplified and analyzed by Illumina sequencing

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
32007972
Reads aligned (%)
78.9
Duplicates removed (%)
9.1
Number of peaks
22844 (qval < 1E-05)

hg38

Number of total reads
32007972
Reads aligned (%)
80.5
Duplicates removed (%)
7.9
Number of peaks
23134 (qval < 1E-05)

Base call quality data from DBCLS SRA