E-GEOD-49988 - Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [PC]

Status
Released on 17 October 2013, last updated on 3 June 2014
Organism
Mus musculus
Samples (21)
Array (1)
Protocols (6)
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.
Experiment type
transcription profiling by array 
Contacts
Citation
Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors. 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. , Europe PMC 24120743
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-49988.idf.txt
Sample and data relationshipE-GEOD-49988.sdrf.txt
Raw data (1)E-GEOD-49988.raw.1.zip
Processed data (1)E-GEOD-49988.processed.1.zip
Array designA-MEXP-724.adf.txt
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