Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
THP1 cells
cell type
acute myeloid leukemia (AML)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using a HighCell# ChIP kit (Diagenode, Liege, Belgium) according to the manufacturer’s instructions. Prior to ChIPseq, DNA was purified with an iPure kit (Diagenode), according to manufacturer’s instructions. To prepare samples for sequencing on the Illumina HiSeq 2500 (Illumina, San Diego, CA), a Microplex Library Preparation Kit (Diagenode) was used to generate libraries from 1ng ChIP DNA. Libraries were then size selected (200-800 base pairs) by adding 0.55x volume of AMPure beads (Beckman Coulter, Pasadena, CA) to the sample, followed by 0.3x volume of AMPure beads to the supernatant. The supernatant was then discarded and the beads washed with 70% ethanol before drying and elution of the size selected library. Library quantitation was performed by Q-PCR using a Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Next, 15pM of the library was used for on board cluster generation in the Rapid Mode of a HiSeq 2500 (Illumina) and then paired end 75 or 101 base pair sequencing was performed using a TruSeq Rapid SBS Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
53235663
Reads aligned (%)
98.3
Duplicates removed (%)
27.3
Number of peaks
1122 (qval < 1E-05)

hg19

Number of total reads
53235663
Reads aligned (%)
97.4
Duplicates removed (%)
27.7
Number of peaks
582 (qval < 1E-05)

Base call quality data from DBCLS SRA