Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX2

Cell type

Cell type Class
Blood
Cell type
SEM
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
RUNX2
cell line
Leukemia cell line (SEM)
treatment
N/A
cell type
Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
chip antibody
RUNX2 (CST 8486/1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP. For ChIP-rx fixed SEM cells were mixed at a 4:1 ratio with fixed Drosophila S2 cells prior to sonication. DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
56790612
Reads aligned (%)
69.9
Duplicates removed (%)
21.6
Number of peaks
96944 (qval < 1E-05)

hg38

Number of total reads
56790612
Reads aligned (%)
70.6
Duplicates removed (%)
21.1
Number of peaks
97265 (qval < 1E-05)

Base call quality data from DBCLS SRA