ONTOLOGY SOURCE REFERENCE
Term Source Name	"ArrayExpress"	"EFO"	"NCBITaxon"	"CHEBI"	"SNOMEDCT"	"UBERON"	"BTO"	
Term Source File	"http://www.ebi.ac.uk/arrayexpress/"	"http://www.ebi.ac.uk/efo/efo.owl"	"http://bioportal.bioontology.org/ontologies/47845"	"http://bioportal.bioontology.org/ontologies/50447"	"http://bioportal.bioontology.org/ontologies/46896"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=UBERON"	"http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO"	
Term Source Version	""	""	"47845"	"50447"	"46896"	"Jun 2010"	"Jun 2010"	
Term Source Description	""	""	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Chemical Entities of Biological Interest Ontology"	"Systematized Nomenclature of Medicine - Clinical Terms"	"Uber anatomy ontology"	"BRENDA tissue / enzyme source"	
INVESTIGATION
Investigation Identifier	""
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-38713"
Study Title	"Expression data from intestinal mucosa of patients with ulcerative colitis. 12 of 43 patients are taking the NSAID mesalazine (aka 5-ASA, 5-aminosalicylic acid, mesalamine)."
Study Description	"Patients are scored for extent and duration (evolution) of disease, plus age and sex. [original description: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with periods of active disease followed by remission. We performed a whole-genome transcriptional analysis of colonic biopsies from patients with histologically active and inactive UC, as well as non-inflammatory controls. Ulcerative colitis patients and non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for UC patients were: age between 18 and 65, diagnosis of UC established at least 6 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and histologic score: Mayo sub score >=2 and MATTS >=3 respectively . Inactive disease was also defined by endoscopic and histologic score: Mayo sub score =0 and MATTS <=2 respectively, and a remission state for a minimum of 5 month prior to biopsy collection, and remained inactive for at least 6 months after. Uninvolved mucosa from patients with active UC was defined as a colonic segment with completely normal endoscopic appearance, normal histology, and absence of any previous evidence of active disease. Finally, a total of 43 biopsies were analyzed: 13 healthy controls, 8 inactive UC, 7 non-involved active UC and 15 involved active UC.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2012-11-09"
Study File Name	"s_E-GEOD-38713_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
Study Design Type Term Accession Number	""
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STUDY PUBLICATIONS
Study PubMed ID	"23135761"
Study Publication DOI	"10.1136/gutjnl-2012-303333"
Study Publication Author List	"Planell N, Lozano JJ, Mora-Buch R, Masamunt MC, Jimeno M, Ord‡s I, Esteller M, Ricart E, PiquŽ JM, PanŽs J, Salas A"
Study Publication Title	"Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations."
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STUDY FACTORS
Study Factor Name	"treatment"	"disease extension"	"age years"	"evolution time years"	"sex"	"organ"	"disease state"
Study Factor Type	"treatment"	"disease extension"	"age years"	"evolution time years"	"sex"	"organ"	"disease state"
Study Factor Type Term Accession Number	""	""	""	""	""	"0000062"	""
Study Factor Type Term Source REF	""	""	""	""	""	"UBERON"	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-38713_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	""
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE38713-1"	"P-GSE38713-5"	"P-GSE38713-4"	"P-GSE38713-2"	"P-GSE38713-3"	"P-GSE38713-6"
Study Protocol Type	"bioassay_data_transformation"	"image_aquisition"	"hybridization"	"nucleic_acid_extraction"	"labeling"	"feature_extraction"
Study Protocol Type Term Accession Number	""	""	""	""	""	""
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Study Protocol Description	"ID_REF =  VALUE = log2 GC-RMA expression value"	"Standard Affymetrix protocol using a Gene chip scanner 3000"	"Standard Affymetrix protocol"	"Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions."	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol"	"The data were analyzed with Bioconductor tools in R (http://www.r-project.org) using GC-RMA as normalization method. Next we employ a conservative probe-filtering step excluding those probe sets not reaching a log2 expression values of 5 in at least 1 sample."
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STUDY CONTACTS
Study Person Last Name	"Salas"	"Planell"	"Salas"
Study Person First Name	"Azucena"	"Nœria"	"Azucena"
Study Person Mid Initials	""	""	""
Study Person Email	"asalas1@clinic.ub.es"	""	""
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Study Person Address	"Gastroenterology, IDIBAPS, Rossell—, 149-153, Barcelona, Spain"	""	""
Study Person Affiliation	"IDIBAPS"	""	""
Study Person Roles	"submitter"	""	""
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