Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

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

Attributes by original data submitter

Sample

ENA first public
2020-05-07
ENA last update
2019-12-04
ENA-CHECKLIST
ERC000011
External Id
SAMEA6360271
INSDC center alias
Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR. China
INSDC center name
Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, PR. China
INSDC first public
2020-05-07T17:05:44Z
INSDC last update
2019-12-04T15:13:12Z
INSDC status
public
Submitter Id
E-MTAB-8558:HL60_d2_CTCF_input_1
broker name
ArrayExpress
cell line
HL-60
cell type
leukocyte
common name
human
developmental stage
adult
disease
acute myeloid leukemia
genotype
somatic genotype
organism part
blood
sample name
E-MTAB-8558:HL60_d2_CTCF_input_1

Sequenced DNA Library

library_name
HL60_d2_CTCF_input_1_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10^7 HL-60 cells treated with 10 uM ATRA for 2 and 5 days were harvested for ChIP-seq. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of CTCF, H3K4me3 or H3K27me3 (CST, Boston, USA) were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 4 °C for target protein pull down. The CTCF enriched or H3K4/27me3 modified DNA or input DNA were repaired to 3'-dA overhang and added the ligated adapter. The DNA library was eliminated the unligated adapters and selected the appropriate size for sequence using an Illumina X Ten platform.

Sequencing Platform

instrument_model
HiSeq X Ten

hg38

Number of total reads
17081321
Reads aligned (%)
91.6
Duplicates removed (%)
3.6
Number of peaks
583 (qval < 1E-05)

hg19

Number of total reads
17081321
Reads aligned (%)
90.9
Duplicates removed (%)
4.6
Number of peaks
681 (qval < 1E-05)

Base call quality data from DBCLS SRA