Curated Sample Data


Genome
mm9
Antigen Class
Input control
Antigen
Input control
Cell type Class
Blood
Cell type
Hematopoietic Stem Cells

Cell type information


MeSH Description
Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Attributes by Original Data Submitter


source_name
Tet2-/-: AML1-ETO_IgG control
strain background
C57BL/6
genotype/variation
Tet2-/-: AML1-ETO
cell type
Kit-enriched hematopoietic bone marrow cells
passage number
Passage 10
transduced with
MigR1-AE-IRES-GFP
chip antibody
IgG control (Gamma-globulin (10760815, Pierce))

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Immature myeloid cells (iGMP cells; GFP+, CD11b-, Gr1-, CD16/32+) were sorted from cultures. Genomic DNA was isolated using the AllPrep DNA/RNA micro kit (Qiagen). Duplicate cultures of Tet2fl/fl;AE or Tet2-/-:AE cells grown in vitro for 10 passages after Tet2 disruption were fixed for 10 minutes in 1% formaldehyde dissolved in PBS and the reaction was quenched by addition of glycine to a final concentration of 0.125M. The crosslinked cells were harvested in SDS lysis buffer (100 mM NaCl, 50mM Tris-HCl (pH8.1), 5mM EDTA (pH 8.0), 0.2% NaN3, 0.5% SDS) and nuclei were pelleted and resuspended in IP buffer (100mM Tris-HCl (pH 8.6), 100mM NaCl, 5mM EDTA (pH 8.0), 0.2% NaN3, 5% Triton X-100, 0.3% SDS). The obtained DNA was then sheared to an average size of 150-300bp (Bioruptor, Diagenode) and 40ug of solubilized chromatin was immunoprecipitated with Protein A Sepharose beads (GE healthcare) after overnight incubation with the respective antibodies. Finally, adaptor-ligated libraries were generated from 10ng of precipitated DNA using the NEBNext® DNA library Sample Prep Master kit (New England Biolabs), PCR-amplified (15x PCR cycles) using indexed multiplex primers for illumina sequencing (New England Biolabs), and sequenced on a HiSeq2000 using 50bp single-end sequencing at the National High-Throughput Sequencing Centre (University of Copenhagen).

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
19746358
Reads aligned (%)
96.5
Duplicates removed (%)
15.8
Number of peaks
352 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA