Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
IRF1

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
erythroleukaemia
disease state
erythroleukaemia
cell line
K562
treatment
EPZ-011989
chip antibody
IRF1 (D5E4, Cell Signaling)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and protease inhibitors) and incubated rotating with antibody for a minimum of 12 h at 4 °C. Protein A Dynabeads (Life Technologies) were used to bind the antibody and associated chromatin. After washing and elution from the beads, samples were reverse cross-linked overnight and purified with QIAquick PCR purification kits (Qiagen). Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
33824778
Reads aligned (%)
74.6
Duplicates removed (%)
20.2
Number of peaks
15951 (qval < 1E-05)

hg38

Number of total reads
33824778
Reads aligned (%)
75.5
Duplicates removed (%)
19.6
Number of peaks
16141 (qval < 1E-05)

Base call quality data from DBCLS SRA