Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CLOCK

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 cells
cell line
THP-1
cell type
MLL-AF9 leukemia
chip antibody
anti-KAT13D/Clock (Abcam, ab3517, lot GR130170-5, 1mg/ml)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed as previously described (Kowalczyk, 2012) with minor modifications. Specifically, cells were first fixed in 2mM EGS (Thermo Scientific) for 30 minutes or 1 hour, followed by 1% of formaldehyde for 30 or 15 minutes at room temperature respectively. Chromatin was sonicated to a size less than 500bp and then incubated overnight with appropriate antibodies.  ChIP sequencing (ChIP-Seq) libraries were prepared through the process of DNA end-repair (Epicentre), A-base addition and adaptor ligation using indexed Illumina adaptors followed by enrichment PCR. All enzymatic steps are carried out using enzymes from New England Biolabs. Final libraries were pooled, size selected and sequenced on HiSeq2500 with 25 paired-end reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
36351650
Reads aligned (%)
127.9
Duplicates removed (%)
29.8
Number of peaks
523 (qval < 1E-05)

hg38

Number of total reads
36351650
Reads aligned (%)
129.8
Duplicates removed (%)
29.3
Number of peaks
557 (qval < 1E-05)

Base call quality data from DBCLS SRA