Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2A

Cell type

Cell type Class
Blood
Cell type
ML-2
Primary Tissue
Bone Marrow
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
ML2 cultured cells
cell line
ML2
chip target
MLL1n
antibody
anti-MLL1n (Bethyl #A300-086A lots: 5 or 6)
timepoint
3 days
treatment
DMSO 0.33%

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehyde (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was sheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquot of sheared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used approximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were washed in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads. 1-10 ng of ChIP'ed DNA was used for Illumina compatible library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single or paired end barcodes.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
17524571
Reads aligned (%)
147.5
Duplicates removed (%)
24.6
Number of peaks
364 (qval < 1E-05)

hg38

Number of total reads
17524571
Reads aligned (%)
149.6
Duplicates removed (%)
24.2
Number of peaks
378 (qval < 1E-05)

Base call quality data from DBCLS SRA