Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
WDR5

Cell type

Cell type Class
Blood
Cell type
THP-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
THP-1 leukemia cells
cell line
THP-1
cell type
acute lymphoblastic leukemia cells
antibody
WDR5, ab56919
cell culture condition
10% FBS RPMI1640 in 5% CO2, 37°C

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample Kit . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200-400bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The resulted library was validated by using Agilent Technologies 2100 Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (Illumina GA2) following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
25455562
Reads aligned (%)
65.0
Duplicates removed (%)
21.1
Number of peaks
815 (qval < 1E-05)

hg38

Number of total reads
25455562
Reads aligned (%)
66.8
Duplicates removed (%)
19.8
Number of peaks
737 (qval < 1E-05)

Base call quality data from DBCLS SRA