Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD4

Cell type

Cell type Class
Blood
Cell type
U-937
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma Diffuse Large B Cell

Attributes by original data submitter

Sample

source_name
U937_shKDM6A_CHD4_ChIPSeq
cell line
U937
cell type
Pro-monocytic, human myeloid leukemia cell line
genotype/variation
shKDM6A
chip antibody
CHD4 (Abcam, Cat. ab70469, Clone: 3F2/4)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody. ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer's instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 280 ± 8bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
34667923
Reads aligned (%)
174.5
Duplicates removed (%)
9.9
Number of peaks
669 (qval < 1E-05)

hg38

Number of total reads
34667923
Reads aligned (%)
177.8
Duplicates removed (%)
9.4
Number of peaks
1618 (qval < 1E-05)

Base call quality data from DBCLS SRA