Investigation Title Transcription profiling of human pancreatic tumor and normal samples from the Mayo clinic Comment[Submitted Name] Expression data from Mayo Clinic Pancreatic Tumor and Normal samples Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[AEExperimentType] transcription profiling by array Comment[AEExperimentDisplayName] Transcription profiling by array of human pancreatic tumors Comment[AEMIAMESCORE] 4 Comment[SecondaryAccession] GSE16515 Comment[ArrayExpressReleaseDate] 2009-06-23 Comment[ArrayExpressAccession] E-GEOD-16515 Comment[MAGETAB TimeStamp_Version] 2010-08-02 19:21:49 Last Changed Rev: 13058 Experimental Factor Name disease Experimental Factor Type disease Experimental Factor Term Source REF Person Last Name Wang Person First Name Liewei Person Mid Initials Person Email wang.liewei@mayo.edu Person Phone Person Fax Person Address Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First street SW, Rochester, 55905, USA Person Affiliation Mayo Clinic Person Roles submitter Person Roles Term Source REF 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 2009-06-23 PubMed ID 19732725 Publication DOI 10.1016/j.ccr.2009.07.016 Publication Author List Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L Publication Title FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Publication Status published Publication Status Term Source REF EFO Experiment Description We used microarrays to identify the expression differences of FKBP5 gene between the pancreatic tumor and normal samples. On average normal samples had more FKBP5 expression compared to tumor samples .Experiment Overall Design: This experiment consists of 36 tumor samples and 16 normal samples; a total of 52 samples. 16 samples consist of both tumor and normal expression data, whereas 20 samples consist of only tumor data. Protocol Name P-GSE16515-1 P-GSE16515-5 P-GSE16515-4 P-GSE16515-2 P-GSE16515-3 P-GSE16515-6 Protocol Description ID_REF =
VALUE = GCRMA normalized signal intensity The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes. The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer's instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45C for 16 hr and then washed and stained using the GeneChip Fluidics. RNA extraction was performed as Affymetrix GeneChip expression technical manual (Affymetrix, Inc., Santa Clara, CA). Briefly, total RNA samples were extracted, followed by measurement of the A2260/A280 ratio with at least 1.8 for pure RNA. Quality of the RNA was checked by an Agilent 2100 Bioanalyzer. The Bioanalyzer gel profile exhibited a 28S band that is 2 times more intense than 18S ribosomal RNA. The quality of RNA was assessed by agarose gel electrophoresis. Lableing was performed according to Affymetrix Gene Chip technical manual The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as normalization method. Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_acquisition hybridization nucleic_acid_extraction labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number SDRF File E-GEOD-16515.sdrf.txt Term Source Name ncbitax The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version