Comment[ArrayExpressAccession]	E-GEOD-45377
MAGE-TAB Version	1.1				
Public Release Date	2013-05-27
Investigation Title	Genome-wide mapping of Runx1-bound sites in early B-cell progenitors				
Comment[Submitted Name]	Genome-wide mapping of Runx1-bound sites in early B-cell progenitors
Experiment Description	The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. Gene expression analysis and genome-wide Runx1-occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network in B-cell progenitors governing early B-cell survival and development . ChIP-seq experiments were performed in the proB-cell line BMiFLT3(15-3), stably transduced with the transcription factor Runx1, to identify Runx1-bound sites in early B-cell progenitors.				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Kriebitzsch	Niebuhr	Kriebitzsch	Alawi	Stocking
Person First Name	Neele	Birte	Neele	Malik	Carol
Person Mid Initials	Margarete				
Person Email	neele.kriebitzsch@hpi.uni-hamburg.de				
Person Affiliation	Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology				
Person Address	Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, MartinistraM-CM-^_e 52, Hamburg, Germany				
Person Roles	submitter				
Protocol Name	P-GSE45377-4	P-GSE45377-1	P-GSE45377-3	P-GSE45377-2	
Protocol Description	Illumina Casava 1.8.2 software was used for base calling. Sequence tags were aligned to the mm9 assembly (NCBI Build 37) with Bowtie (v. 0.12.8) reporting only top scoring unique mapping tags. The MACS algorithm was used to identify bound regions by comparing the enrichment of the Runx1-IP sample against a control IgG-IP for background correction. MACS version 1.4.01 was run with all parameters at their default settings, except m-fold, which was set at 8,30, to identify Runx1-bound regions. Genome_build: mm9 Supplementary_files_format_and_content: Bed file identifies Runx1-bound regions	24 hours before DNA extraction, cells were either treated with 0.2 M-5M Tamoxifen to ensure Runx1-ERt2 translocation into the nucleus or treated with the appropriate amount of ethanol as a control.	ChIP experiments using anti-Runx1 or anti-IgG antibodies were performed using the EZ-ChIP Kit (Upstate/Millipore) according to the manufacturerM-bM-^@M-^Ys protocol. Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts M-bM-^IM-%70 bps.DNA fragments between 350-550 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 1200 using a High Sensitivity DNA Kit (Agilent).	Cells were routinely grown in M-NM-1-MEM with 10% FCS, glutamine and sodium pyruvate.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol	
Experimental Factor Name	CHIP-SEQ ANTIBODY				
Experimental Factor Type	chip-seq antibody				
Comment[SecondaryAccession]	GSE45377				
Comment[GEOReleaseDate]	2013-05-27				
Comment[ArrayExpressSubmissionDate]	2013-03-21				
Comment[GEOLastUpdateDate]	2013-05-27				
Comment[AEExperimentType]	ChIP-seq				
Comment[AdditionalFile:Data1]	GSE45377_Runx_IgG_peaks.bed				
Comment[SecondaryAccession]	SRP019917				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR789240-SRR789249				
SDRF File	E-GEOD-45377.sdrf.txt