Comment[ArrayExpressAccession]	E-GEOD-34586
MAGE-TAB Version	1.1							
Public Release Date	2013-04-02
Investigation Title	Comparison of the transcripts in control and Blimp-1-deficient keratinocytes							
Comment[Submitted Name]	Comparison of the transcripts in control and Blimp-1-deficient keratinocytes
Experiment Description	We performed microarray analysis to examine the differential gene expression profiles between Prdm1 (Blimp-1)-deleted and control keratinocytes. Keratinocytes isolated from Prdm1-floxed K5-CreER positive (CKO) mice were cultured in the presence of 4OHT to induce deletion of the Prdm1 allele in vitro. Prdm1-floxed K5-CreER positive (CKO) keratinocytes treated with the ethanol solvent control (EtOH) or Prdm1-floxed K5-CreER negative (control) keratinocytes treated with 4OHT or EtOH served as controls. Microarray analyses revealed that there were 93 genes up-regulated and 109 genes down-regulated by more than 2-fold in the CKO + 4OHT group in comparison with the CKO + EtOH, Ctrl + 4OHT or Ctrl + EtOH groups. Several corneocytes-related genes, including Rptn, Lce1f, Krt1 and Lce1d, are significantly down-regulated and several cytokines/chemokines, including Cxcl1, Cxcl2, Cxcl5 and Il24, are significantly up-regulated upon the deletion of Prdm1 in vitro. We analyzed the transcription profiles in control and Blimp-1-deficient keratinocytes using the GeneChip® Mouse Expression Array 430A.							
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	Chiang	Chiang	Lin	Lin				
Person First Name	Ming-Feng	Ming	I	K				
Person Mid Initials		F	Y	I				
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	Academia sinica							
Person Address	Genomics Research Center, Academia sinica, 128 Academia Road, Section 2, Taipei, Taiwan							
Person Roles	submitter							
Protocol Name	P-GSE34586-1	P-GSE34586-6	P-GSE34586-3	P-GSE34586-8	P-GSE34586-7	P-GSE34586-2	P-GSE34586-4	P-GSE34586-5
Protocol Description	ID_REF =  VALUE = Signal intensity	The biotinylated cRNAs were hybridized to GeneChip® Mouse Expression Array 430A.	Tail skin keratinocytes were cultured in serum-free medium, CnT-07 (CELLnTEC), and rat collagen I coated plates. Culture medium was refreshed on day 3 and cells were collected on day 5.	Data were processed by the RMA algorithm using GeneSpring GX11.	Microarray was scanned and images were acquired by GeneChip® Scanner 3000.	4-hydroxytamoxifen (4OHT) or ethanol (EtOH, solvent control) were added to culture medium from day 1 to day 3.	Total RNA was isolated using the Qiagn RNeasy® Mini kit, followed by using the Qiagen RNase-Free DNase Set to remove DNA. The isolation procedure was performed per the manufacturer's instructions.	Microarray was performed according to the protocol provided by the manufacturer (3' IVT express kit, Affymetrix). Total RNAs were used as the template to generate double-strand cDNAs. Total RNAs were degraded and double-strand cDNAs were purified by cDNA Cleanup Spin Column (Qiagen). cRNAs with biotin-conjugated nucleotide analog were generated and amplified by in vitro transcription using T7 RNA polymerase.
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	TREATMENT							
Experimental Factor Type	treatment							
Comment[SecondaryAccession]	GSE34586							
Comment[GEOReleaseDate]	2013-04-02							
Comment[ArrayExpressSubmissionDate]	2011-12-20							
Comment[GEOLastUpdateDate]	2013-04-04							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-34586.sdrf.txt