Comment[ArrayExpressAccession]	E-GEOD-46270
MAGE-TAB Version	1.1						
Public Release Date	2013-05-06
Investigation Title	Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo						
Comment[Submitted Name]	Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo
Experiment Description	Bcl11a is a transcription factor known to regulate lymphoid and erythroid development. Recent bioinformatic analysis of global gene expression patterns has suggested a role for Bcl11a in the development of dendritic cell (DC) lineages. We tested this hypothesis by analyzing the development of DC and other lineages in Bcl11a(-/-) mice. We show that Bcl11a is required for expression of IL-7 receptor (IL-7R) and Flt3 in early hematopoietic progenitor cells. The loss of IL-7R(+) common lymphoid progenitors accounts for previously described lymphoid defects in Bcl11a(-/-) mice. In addition, we found severely decreased numbers of plasmacytoid dendritic cells (pDCs) in Bcl11a(-/-) fetal livers and in the bone marrow of Bcl11a(-/-) fetal liver chimeras. Moreover, Bcl11a(-/-) cells show severely impaired in vitro development of Flt3L-derived pDCs and classical DCs (cDCs). In contrast, we found normal in vitro development of DCs from Bcl11a(-/-) fetal liver cells treated with GM-CSF. These results suggest that the persistent cDC development observed in Bcl11a(-/-) fetal liver chimeras reflects derivation from a Bcl11a- and Flt3-independent pathway in vivo. We compared global gene expression by microarray for donor-derived wild-type and Bcl11a(-/-) populations isolated from chimeric bone marrow to identify Bcl11a target genes that explain its role in hematopoietic progenitors. GMP and MPP populations were sorted from fetal liver chimeras and pooled by donor genotype. RNA was isolated using an RNAqueous-Micro Kit (Ambion) and submitted for amplification, labeling and hybridization. Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).						
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	Wu	Wu	Satpathy	KC	Murphy		
Person First Name	Xiaodi	Xiaodi	Ansuman	Wumesh	Kenneth		
Person Mid Initials			T		M		
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	Washington University/HHMI						
Person Address	Washington University/HHMI, 4940 Parkview Pl, St. Louis, Missouri, USA						
Person Roles	submitter						
Protocol Name	P-GSE46270-1	P-GSE46270-5	P-GSE46270-6	P-GSE46270-2	P-GSE46270-3	P-GSE46270-4	P-GSE46270-7
Protocol Description	Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR). ID_REF =  VALUE = log2 RMA signal intensity	Biotinylated cRNA was prepared using an Ovation PicoSL kit (NuGEN).	cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix).	After 4 weeks, bone marrow was isolated by grinding and Histopaque-1119 (Sigma-Aldrich) centrifugation and sorted by flow cytometry.	B6.SJL mice were lethally irradiated (1200 rad) and injected intraorbitally with 4e6 fetal liver cells isolated from WT or Bcl11a(-/-) fetuses.	Total RNA was isolated using an RNAqueous-Micro Kit (Ambion) according to manufacturer's instructions.	Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CELL TYPE	GENOTYPE					
Experimental Factor Type	cell type	genotype					
Comment[SecondaryAccession]	GSE46270						
Comment[GEOReleaseDate]	2013-05-06						
Comment[ArrayExpressSubmissionDate]	2013-04-22						
Comment[GEOLastUpdateDate]	2013-05-08						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-46270.sdrf.txt