GSM5858397: MV4;11 MEN1-M327 DMSO MLL1-ChIP DMSO; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
KMT2A
Cell type
Cell type Class
Blood
Cell type
MV-4-11
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous
Attributes by original data submitter
Sample
source_name
MLL-AF4 rearranged human leukemia cell line (MV4;11)
cell line
MV4;11
chip-antibody
anti-MLL1 (Rb)
antibody manufacturer
Bethyl laboratories
antibody catalog number
A300-086A
treatment molecule
DMSO
treatment timepoint
4d
treatment dose
0.10%
Sequenced DNA Library
library_name
GSM5858397
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny). The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (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 cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared 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 aproximately 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 wased 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 compatibl library generation using ThruPlex DNA-seq kit with 12 to 14 cycles of amplification with single or paired end barcodes