Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K9me3

Cell type

Cell type Class
Blood
Cell type
Acute myeloid leukemia
NA
NA

Attributes by original data submitter

Sample

source_name
AML_MA9+SETDB1_ChIPseq_H3K9me3
tissue source
bone marrow
cell line background
MLL-AF9 (MA9) acute myeloid leukemia cell line
retroviral transduction
MLL-AF9 + SETDB1
chip antibody
H3K9me3 (Active Motif 39162, lot # 21518003)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1%paraformaldehyde, the fixation was quenched with glycine, and the fixed cells were snap-frozen and stored at -80C. Cells were slow thawed on ice for 15 minutes, then lysed in 1% SDS lysis buffer. Chromatin was sheared on a water bath sonicator, and IPs were performed using the indicated antibodies and protein G magnetic beads. DNA was decrosslinked and purified using Qiagen PCR purification kit. Libraries were prepped using 5ng DNA and the iDeal library prep kit. Amplification cycles of the library preps were optimized using qPCR.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
66689393
Reads aligned (%)
94.8
Duplicates removed (%)
23.9
Number of peaks
417 (qval < 1E-05)

mm9

Number of total reads
66689393
Reads aligned (%)
94.5
Duplicates removed (%)
26.1
Number of peaks
439 (qval < 1E-05)

Base call quality data from DBCLS SRA