Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
K562 cells
cell line
K562
treatment
Non-treated (NHS)
antibody
no antibody, fragmented total chromatin
antibody_epitope
--

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After tretments, the cells were cross-linked with 1% fromaldehyde, quenched with glycine, washed twice with PBS and flash-frozen. The ChIP-experiments were conducted as described for GSE43579 (Vihervaara et al., Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic celss, 2013, PNAS, 110: 36, E3388-3397). The libraries were generated with Nextera DNA Sample Preparation kit (Illumina). Paired-end sequencing (HiSeq PE100) was performed with Illumina.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
28957862
Reads aligned (%)
81.2
Duplicates removed (%)
1.5
Number of peaks
907 (qval < 1E-05)

hg19

Number of total reads
28957862
Reads aligned (%)
80.5
Duplicates removed (%)
1.7
Number of peaks
493 (qval < 1E-05)

Base call quality data from DBCLS SRA