Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2A

Cell type

Cell type Class
Blood
Cell type
OCI-AML3
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
OCI-AML-3 cultured cells
cell line
OCI-AML-3
timepoint
4 days
treatment
VTP-50469 330nM
chip target
MLL
chip antibody
anti-MLL1n (A300-086A, Bethyl)
seqbatch
181004

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
DMSO or VTP-50469 treated cells were crosslinked with 1% methanol-free formaldehyde (ThermoFisher) for 7-10 min at room temperature, followed by quenching with 100 mM Tris pH8.0 and 25 mM Glycine, and the cells were lysed in SDS buffer. Cytoplasm was lysed using 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1% SDS for 10 min and nuclei were precipitated by centrifugation at 10,000´g. Nuclei were resuspended in 66 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM EDTA, 1.7% Triton X-100, 0.5% SDS and sheared using E100S (Covaris) to chromatin fragments of 200-400 base-pair DNA size. 1-10 ng of DNA was used in preparation of Illumina-compatible libraries using ThruPlex DNA kit (Rubicon Genomics) Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) was used to obtain 1-5´107 unique sequencing paired-end tags

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
29604355
Reads aligned (%)
62.5
Duplicates removed (%)
68.2
Number of peaks
7515 (qval < 1E-05)

hg38

Number of total reads
29604355
Reads aligned (%)
65.0
Duplicates removed (%)
67.1
Number of peaks
7581 (qval < 1E-05)

Base call quality data from DBCLS SRA