Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ASH1L

Cell type

Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous

Attributes by original data submitter

Sample

source_name
ASH1_K562
cell line
leukemia cell line K562
chip antibody
anti-ASH1 (made in-house)
chip antibody batch
#3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 1x108 K562 cells were fixed by 10% formaldehyde in 50 mM Hepes-KOH, pH7.5, 100 mM NaCl, 1 mM EDTA, ph8.0, 0.5 mM EGTA, pH8.0 for 10 min at room temperature, quenched by one tenth volume of 2.5 M Glycine, rinsed sequentially with LB1 (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, pH8.0), and resuspended in LB3 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, pH8.0 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) containing Protease Inhibotor Cocktail (Roche). Cell suspension was then sonciated by Covaris S2 Acoustic Solbilyzer with Duty Cycle 20%, Intensity 5, Cycles per Burst 200, and 20-30 cycles. Lysates were cleared by centrifugation, and immunoprecipitated with anti-ASH1 antibodies fixed on Dynabeads M-280 sheep anti-rabbit/mouse IgG (Invitrogen), washed with LiCl buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40, 1% Na-Deoxycholate) and then with TE, and eluted in 1% SDS, 0.1 M NaHCO3. After overnight de-crosslinking, DNA was purified with PCR Cleanup column (QIAGEN). Fragment sizes were checked by 2100 BioAnalyzer (Agilent). Sequencing libraries were constructed using ChIP-Seq Sample Prep Kit (Illumina) according to the manufacture's protocol.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
43025549
Reads aligned (%)
92.7
Duplicates removed (%)
5.8
Number of peaks
1699 (qval < 1E-05)

hg38

Number of total reads
43025549
Reads aligned (%)
94.1
Duplicates removed (%)
5.1
Number of peaks
2729 (qval < 1E-05)

Base call quality data from DBCLS SRA