Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
HL-60
Primary Tissue
Blood
Tissue Diagnosis
Leukemia

Attributes by original data submitter

Sample

source_name
hl60
cell line
HL-60 cell
cell type
human leukemia cells
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were digested by micrococcal nuclease and DNA complexes were isolated with antibody A ChIP-seq library was prepared from approximately 20 ng of ChIP-DNA and an input sample from a mixture of 3 ChIP operations. The concentration and integrity of the DNA sample was checked by gel electrophoresis. The selected libraries for a fragment size of 100 bp to 500 bp were amplified using PCR. ChIP-seq libraries were run on a HiSeq next-generation sequencer (Illumina, San Diego, CA, USA). After abandonment of polluted reads, low-quality reads, and reads with N > 5%, sequenced-50 base short single reads were mapped to the human genome, and the peaks were identified by Model-based Analysis of ChIP-Seq S14 software.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
21999288
Reads aligned (%)
99.2
Duplicates removed (%)
5.0
Number of peaks
280 (qval < 1E-05)

hg19

Number of total reads
21999288
Reads aligned (%)
98.5
Duplicates removed (%)
6.5
Number of peaks
470 (qval < 1E-05)

Base call quality data from DBCLS SRA