Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
HL-60
cell line
HL-60
genotype
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq experiments were performed using c-Kit+ HSPCs or HL-60 cell lines. Cells were fixed in PBS with 1% formaldehyde (Thermo Fisher Scientific) for 10 min at room temperature with gentle mixing. The reaction was stopped by adding glycine solution (10x) (Cell Signaling Technology) and incubating for 5 minutes at room temperature, and the cells were washed in cold PBS twice. The cells were then processed with SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling Technology) and Covaris E220 (Covaris) according to the manufacturer's protocol. The antibodies used for ChIP are as follows: STAG1 (Protein Tech, 14015-1-AP), STAG2 (Novus, NBP1-30472), SMC1 (Abcam, ab9262), CTCF (Cell Signaling Technology, D31H2), RUNX1 (Abcam, 23980), total Pol II (CST, D8L4Y), Ser5-P Pol II (Abcam, ab5408), H3K27ac (Cell Signaling Technology, D5E4), H3K27me3 (Cell Signaling Technology, C36B11), H3K4me1 (Cell Signaling Technology, D1A9), or H3K4me3 (Cell Signaling Technology, C42D8). ChIP-seq libraries were constructed using ThruPLEX DNA-seq kit (Takara) according to the manufacturer's protocol, and then subjected to sequencing using HiSeq 2500 or NovaSeq 6000 (Illumina).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
42276070
Reads aligned (%)
98.6
Duplicates removed (%)
18.5
Number of peaks
1031 (qval < 1E-05)

hg19

Number of total reads
42276070
Reads aligned (%)
97.8
Duplicates removed (%)
18.9
Number of peaks
854 (qval < 1E-05)

Base call quality data from DBCLS SRA