Comment[ArrayExpressAccession]	E-GEOD-38336
MAGE-TAB Version	1.1								
Public Release Date	2013-12-01
Investigation Title	Gene expression signatures of Meis1 conditional knockout hematopoietic stem cells								
Comment[Submitted Name]	Gene expression signatures of Meis1 conditional knockout hematopoietic stem cells
Experiment Description	Meis1 encodes a TALE family homeodomain protein that was first identified as a common retroviral integration site in mouse BHX2 myeloid leukemia. It functions as a DNA binding co-factor of Hox proteins through interacting with Pbx, a member of another TALE family protein. Moreover, Meis1 homozygous knockout mice are embryonic lethal, showing significant defects in vasculogenesis, eye development and hematopoiesis. Severe defects were also observed in adult hematopoiesis by conditional inactivation of Meis1 in vivo. Meis1 is critical to maintain the balance between enter and exit from cell cycles of hematopoietic stem cells (HSCs), indicating that Meis1 regulates self-renewal and quiescence of HSCs. Total RNA was isolated from KSL cells obtained from poly(I:C)-treated Mx1-Cre Meis1fl/fl and sham-treated Meis1fl/fl mice.								
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	Nakamura	Ariki	Morikawa	Hidano	Nakatake	Matsuzaki	Nakauchi	Nakamura	Goitsuka
Person First Name	Takuro	R	S	S	M	Y	H	T	R
Person Email	takuro-ind@umin.net								
Person Affiliation	Japanese Foundation for Cancer Research								
Person Phone	81-3-3570-0462								
Person Address	The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, Japan								
Person Roles	submitter								
Protocol Name	P-GSE38336-1	P-GSE38336-4	P-GSE38336-5	P-GSE38336-2	P-GSE38336-3	P-GSE38336-6			
Protocol Description	The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. ID_REF =  VALUE = Agilent Feature Extraction gProcessedSignal	Cyanine-3 (Cy3) labeled cDNA was prepared from 10 ng RNA using the WT-Ovation Pico RNA Amplification System (Agilent) and Genomic Enzymatic Labeling kit (Agilent) according to the manufacturer's instructions.	1.5 ug of Cy3-labelled cDNA was hybridized to Agilent Whole Mouse Genome Oligo Microarrays (4 x 44K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.	Mx1-Cre positive Meis1fl/fl and Nx1-Cre negative Meis1fl/fl mice mice at the age of 4-8 weeks were injected i.p. with 1.5 ug/g of poly(I:C) 4 times at 1-day interval to activate interferon gene.	KSL cells were sorted using FACSAreaII and antibodies. Total RNA was isolated using the Qiagen RNeasy micro kit (Qiagen, Hilden, Germany) according to manufacturer's protocol.	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).			
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol			
Experimental Factor Name	GENOTYPE								
Experimental Factor Type	genotype								
Comment[SecondaryAccession]	GSE38336								
Comment[GEOReleaseDate]	2013-12-01								
Comment[ArrayExpressSubmissionDate]	2012-05-30								
Comment[GEOLastUpdateDate]	2013-12-01								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-38336.sdrf.txt