Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2A

Cell type

Cell type Class
Blood
Cell type
SHI-1
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
Commercially available cell line
cell line
SHI1
cell type
Human leukemia cell
chip antibody
MLL1 (Bethyl, A300-086A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP were performed as described in (Milne et al., 2009) with the following modifications: The cells were fixed using a 1% formaldehyde (FA) fixation protocol for 10 min, while a 45 min, 2mM disuccinimidyl glutarate (DSG) and a 30 min 1% FA double fixation protocol was used for all other antibodies. The antibodies used included SHARP1 (a mixture of H-72 Santa-Cruz, 12688-1-AP Proteintech, and ab175544 Abcam), H3K79me2 (Millipore, 04-835), H3K79me3 (Diagenode, pAb-068-050), MLL1 (Bethyl, A300-086A), H3K4me3 (Active Motif, 39159), H3K27me3 (Millipore, 07-499), H3K27ac (Millipore, 07-360), LEDGF (Bethyl, A300-848A), MEN1 (Bethyl, A300-105A). Fixed chromatin samples were fragmented using a Bioruptor sonicator (Diagenode) for 30 min at high in a constantly circulating 4C water bath to an average size of 200-500bps. Antibody:chromatin complexes were collected with a mixture of protein A and Protein G Dynabeads (Life Technologies) collected with a magnet, and washed 2X with a solution of 50mM HEPES-KOH, pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, and 0.7% Na-Deoxycholate. After a TE wash, samples were eluted, RNase and Proteinase K treated, and purified using a QIAGEN PCR purification kit. RNA was extracted using RNeasy kit (QIAGEN). ChIP-seq libraries were prepared using Next ChIP-Seq library prep reagent set (New England Biolabs), and multiplexed (New England Biolabs). RNA-seq libraries were prepared using Illumina Tru-Seq Stranded Total RNA with Ribo-Zero Gold kit protocol, according to the manufacturer's instructions (Illumina, San Diego, California, USA).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
22861777
Reads aligned (%)
59.1
Duplicates removed (%)
69.8
Number of peaks
359 (qval < 1E-05)

hg38

Number of total reads
22861777
Reads aligned (%)
61.3
Duplicates removed (%)
68.9
Number of peaks
468 (qval < 1E-05)

Base call quality data from DBCLS SRA