Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Blood
Cell type
Bone marrow mononuclear cells
NA
NA

Attributes by original data submitter

Sample

source_name
Bone marrow mononuclear cells
cell type
AML blast cells
translocation
MLL-AF9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was harvested and ChIPs were performed as described (Mandoli A, GDATA, 2014). ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the HiSeq 2000 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
50140825
Reads aligned (%)
16.2
Duplicates removed (%)
17.8
Number of peaks
23079 (qval < 1E-05)

hg19

Number of total reads
50140825
Reads aligned (%)
16.1
Duplicates removed (%)
17.8
Number of peaks
23009 (qval < 1E-05)

Base call quality data from DBCLS SRA