Comment[ArrayExpressAccession]	E-GEOD-49988
MAGE-TAB Version	1.1					
Public Release Date	2013-10-17
Investigation Title	Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [PC]					
Comment[Submitted Name]	Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [PC]
Experiment Description	Primary hematopoietic cells from mouse bone marrow were sorted and hybridised expression microarrays as part of a study investigating the differentiation of a multipotential cell-line to erthroid and myeloid fates. We used the paradigmatic 'GATA-PU.1 axis’ to explore, at systems-level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIPSeq of GATA1, GATA2 and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (i)  differential complexity of sequence motifs bound by GATA1, GATA2 and PU.1; (ii) the scope and interplay of the GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (iii) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression and (iv) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry.  This 'rubric' exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis. Primary hematopoietic cells from mouse bone marrow sorted using the dissection as described by Pronk et al (2007,Cell Stem Cell) where lin was defined as B220, CD3, CD4, CD8, CD41, Mac1, Gr1, Ter119.					
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	Soneji	Enver	Soneji			
Person First Name	Shamit	Tariq	Shamit			
Person Email	shamit.soneji@med.lu.se					
Person Affiliation	BMC					
Person Address	BMC, Sölvegatan 19, Lund, Sweden					
Person Roles	submitter					
Protocol Name	P-GSE49988-1	P-GSE49988-4	P-GSE49988-5	P-GSE49988-2	P-GSE49988-3	P-GSE49988-6
Protocol Description	The scanned images were analyzed with Feature Extraction Software (Agilent v10.7.1.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. ID_REF =  VALUE = Normalized signal intensity	Total RNA (150ng) and Agilent One-Color RNA Spike-In were reverse-transcribed and linearly amplified in the presence of Cy3-labeled CTP using Low RNA Input One-Color Kit (Agilent) following Agilent protocols, to generate Cy3-labeled cRNA for hybridisation to high-density microarrays. Quality and yield/specific activity of cRNA were determined using RNA 6000 Nano kit and spectrophotometer (NanoDrop ND- 1000). All samples generated comparable quality cRNA profiles, with specific activities in the range of 10.3 to 12.2 pmol Cy3/mg cRNA.	Each Cy3-labeled cRNA sample (1.6ug as per NanoDrop reading) was hybridised to an individual 44K subarray of 4x44K high-density microarray slide (Whole Mouse Gene Expression Microarrays, Agilent), washed, scanned and feature-extracted as per Agilent protocols.	Cells were extracted from mouse bone marrow and sorted according to the markers stated in the sample descriptions.	Total RNA was isolated from samples using TRIzol reagent, and RNA concentration and integrity were determined using RNA 6000 Nano RNA kit (Agilent) on BioAnalyzer 2100 (Agilent).	Scanning and feature extraction was performed as per Agilent protocols
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	FRACTION					
Experimental Factor Type	fraction					
Publication Title	Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors.					
Publication Author List	May G, Soneji S, Tipping AJ, Teles J, McGowan SJ, Wu M, Guo Y, Fugazza C, Brown J, Karlsson G, Pina C, Olariu V, Taylor S, Tenen DG, Peterson C, Enver T					
PubMed ID	24120743					
Publication DOI	10.1016/j.stem.2013.09.003					
Comment[SecondaryAccession]	GSE49988					
Comment[GEOReleaseDate]	2013-10-17					
Comment[ArrayExpressSubmissionDate]	2013-08-19					
Comment[GEOLastUpdateDate]	2013-10-17					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-49988.sdrf.txt