Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
Leukemia
MeSH Description
A progressive, malignant disease of the blood-forming organs, characterized by distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemias were originally termed acute or chronic based on life expectancy but now are classified according to cellular maturity. Acute leukemias consist of predominately immature cells; chronic leukemias are composed of more mature cells. (From The Merck Manual, 2006)

Attributes by original data submitter

Sample

source_name
In-vivo leukemia cells from spleen
disease state
MLL-AF10 leukemia
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
0.7% Fixed leukemia cells were lysed for 20 min in nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) containing freshly added 1x proteinase inhibitor cocktail (Roche) on ice, then sonicated to generate DNA fragments of 150-500 base pair using a Diagenode Bioruptor XL sonicator for a total duration of 60 cycles (30 seconds ON and 30 seconds OFF). The soluble chromatin was diluted 10-fold with ChIP dilution buffer (20m M Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.01% SDS, 1% Triton-x 100) containing 1x proteinase inhibitor cocktail, and the diluted duration of 60 cycles (30 seconds ON and 30 seconds OFF). The soluble chromatin was diluted 10-fold with ChIP dilution buffer (20m M Tris-HCl pH 8.0, 150 chromatin (1 mL equivalent to 2 million cells) was subjected to immunoprecipitation using various ChIP grade antibodies coupled with protein A magnetic beads (Invitrogen). DNA was used for ChIP-seq library construction based on manufacturer's protocol with modifications to account for limited number of cells (Schmidt et al., 2009).

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
19264665
Reads aligned (%)
76.4
Duplicates removed (%)
11.0
Number of peaks
299 (qval < 1E-05)

mm9

Number of total reads
19264665
Reads aligned (%)
76.3
Duplicates removed (%)
11.0
Number of peaks
343 (qval < 1E-05)

Base call quality data from DBCLS SRA