Antigen

Antigen Class

Histone

Antigen

H3K9ac

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)

Sample

source_name

Leukemic cells

cell type

Leukemic cells

genotype

Gfi1 KI/wt

mouse strain

C57/BL6 NUP98-HOXD13

antibodies

ab4441; Abcam

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies) Sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

128677852

Reads aligned (%)

92.4

Duplicates removed (%)

16.8

Number of peaks

18944 (qval < 1E-05)

mm9

Number of total reads

128677852

Reads aligned (%)

92.3

Duplicates removed (%)

17.1

Number of peaks

18969 (qval < 1E-05)