Investigation Title	Transcription profiling of the islets from Pdx1+/- mice compared to islets isolated from Pdx1 +/+ littermates
Comment[Submitted Name]	Pdx1 transcriptional targets in primary mouse islets.
Experimental Design	genetic_modification_design	co-expression_design	dye_swap_design	transcription profiling by array
Experimental Design Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	EFO
Comment[AEMIAMESCORE]	3
Comment[SecondaryAccession]
Comment[ArrayExpressReleaseDate]	2009-12-02
Comment[ArrayExpressAccession]	E-MTAB-127
Comment[MAGETAB TimeStamp_Version]	2010-08-11 17:27:33 Last Changed Rev: 13058
Experimental Factor Name	GENOTYPE
Experimental Factor Type	genotype
Experimental Factor Term Source REF
Person Last Name	Sachdeva	Groff	Schug	White	Stoffers	Khoo	Claiborn
Person First Name	Mira	David	Jonathan	Peter	Doris	Cynthia	Kathryn
Person Mid Initials							
Person Email	miras@mail.med.upenn.edu	dgroff@mail.med.upenn.edu	jschug@mail.med.upenn.edu	pwhite@mail.med.upenn.edu	stoffers@mail.med.upenn.edu	cynthiakhoo@gmail.com	kcc2@mail.med.upenn.edu
Person Phone	(215) 573-6647	(215) 898-0209	(215) 898-0773	(215) 898-0773	(215) 573-5413	(215) 573-6647	(215) 573-6647
Person Fax
Person Address	720 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104-6145. USA	720 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104-6145. USA	752B CRB, 415 Curie Blvd, Philadelphia, PA 19104-6145	726 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104-6145. USA	720 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104-6145. USA	720 Clinical Research Building, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104-6145. USA
Person Affiliation	Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania	Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania	University of Pennsylvania Functional Genomics Core	University of Pennsylvania Functional Genomics Core	Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania	Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania	Department of Genetics and Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania
Person Roles	investigator	submitter	investigator	investigator	investigator	investigator	investigator
Person Roles Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date	2009-12-02
PubMed ID	19855005
Publication DOI	19855005
Publication Author List	Sachdeva MM, Claiborn KC, Khoo C, Yang J, Groff DN, Mirmira RG, Stoffers DA.
Publication Title	Pdx1 (MODY4) regulates pancreatic beta cell susceptibility to ER stress
Publication Status	journal_article
Publication Status Term Source REF	The MGED Ontology
Experiment Description	The aim of this experiment was to use global gene expression profiling to identify genes that are differentially expressed in the islets from Pdx1+/- mice compared to islets isolated from Pdx1 +/+ littermates. The Pdx1 null mutation consists of a nuclear targeted _-galactosidase cassette fused in-frame with the N terminus of PDX-1.
Protocol Name	P-MTAB-4792	P-MTAB-4793	P-MTAB-4794	P-MTAB-4795	P-MTAB-4798	P-MTAB-4797
Protocol Type	dissect	nucleic_acid_extraction	labeling	hybridization	transformation_protocol_series	feature_extraction
Protocol Description	Mice were anaesthetizied and the pancreas was inflated with cold 1X Hanks buffer, dissected from the abdomen and minced for 2 minutes. Islets were released from acinar tissue by digestion with collagenase (Crescent Chemical Co. Inc.) at 37C for 10-15minutes. Islets were then purified through a Ficoll gradient and then subjected to two rounds of hand picking.	Place Islets in 1ml Trizol. Snap Freeze and store at -80C. Thaw samples and vortex for 30 seconds. Incubate for 5 minutes @ room temperature. Add 0.2mls chlorform. Shake 15s. Incubate @ room temp 2-3min. Centrifuge 5m 1200g @4C. Transfer Aqueous phase to new tube, add 1 volume (350-600ul) 70% ethanol and mix by inverting. Continue following RNeasy (Qiagen) RNA extaction protocol starting at column step.	Approximately 500 ng of total RNA was amplified using the MessageAmpª II aRNA Amplification Kit (Ambion, TX). After amplification 2.5 _g of aRNA was indirectly labeled using amino-allyl dUTP and anchored oligo(d)T prime reverse transcription. The cDNA was purified using the MinElute PCR Purification Kit (Qiagen, CA), eluted in coupling buffer (0.1M Sodium Bicarbonate, pH 9) and coupled with the appropriate Cy3 or Cy5 fluorescent label (CyªDye, Amersham Pharmacia Biotech Ltd, NJ). , combined and purified using the (Qiagen, CA).	The samples were then cooled to 42¡C and an equal volume of 2 x hybridization buffer (50% formamide, 10 x SSC, and 0.2% SDS) was added, mixed, and applied to the Mouse PancChip 6.1 cDNA microarray slide	Median foreground intensities were obtained for each spot and imported into the mathematical software package ÒRÓ, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White. The ratio of expression for each element on the array was calculated in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). The dataset was filtered to remove positive control elements (Cy3 anchors and SpotReport elements) and any elements that had been manually flagged as bad. The M values were then normalized by the print tip loess method using the ÒmarrayÓ microarray processing package in ÒRÓ. Statistical analysis was performed in ÒRÓ using both the LIMMA and SAM packages	GenePix Feature Extraction quantification
Protocol Parameters					marray version;limma version;Script version;R version;signal column;background column;SAM version;spots used for loess curve;	software version;
Protocol Hardware
Protocol Software
Protocol Contact
Protocol Term Source REF						The MGED Ontology
SDRF File	E-MTAB-127.sdrf.txt
Term Source Name	EFO	NCBI Taxonomy	NCI_thesaurus		The MGED Ontology	ArrayExpress	The MGED Ontology	EFO
Term Source File	http://www.ebi.ac.uk/efo/	http://www.ncbi.nlm.nih.gov/Taxonomy/	ncithesaurus.obo.alt		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/
Term Source Version