ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"NCBITAXON"	"UO"	"DOID"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/UO"	"http://data.bioontology.org/ontologies/DOID"	
Term Source Version	"78"	"111"	"2"	"42"	"399"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Units of Measurement Ontology"	"Human Disease Ontology"	
INVESTIGATION
Investigation Identifier	""
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-14442"
Study Title	"Gene expression analysis in gut biopsies of Crohn's Disease patients and patients with Spondylarthropathy"
Study Description	"A focussed microarray chip was constructed specifically for studying basal colonic gene expression in patients with Spondyloarthropathy (SpA) and Crohn's disease (CD) (ref: PMID 16476712). These focus microarrays were used 1) to study common changes in gene expression between SpA and CD, providing early markers in the follow-up study of patients with SpA and particularly these patients that evolve into clinically overt CD; and 2) to identify new candidate genes for CD by integrating gene expression data with genetic information. Keywords: Crohn's Disease, Spondylarthropathy, biopsies This experiment was done in a dye-swap design in which all samples of interest were compared to a pooled sample."
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2010-05-01"
Study File Name	"s_E-GEOD-14442_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	"16476712"
Study Publication DOI	"10.1136/ard.2005.047738"
Study Publication Author List	"Laukens D, Peeters H, Cruyssen BV, Boonefaes T, Elewaut D, De Keyser F, Mielants H, Cuvelier C, Veys EM, Knecht K, Van Hummelen P, Remaut E, Steidler L, De Vos M, Rottiers P"
Study Publication Title	"Altered gut transcriptome in spondyloarthropathy."
Study Publication Status	""
Study Publication Status Term Accession Number	""
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STUDY FACTORS
Study Factor Name	"rna from unaffected colon biopsies.  patients clinical characteristics"	"rna from unaffected colon biopsies. patients clinical characteristics"
Study Factor Type	"rna from unaffected colon biopsies.  patients clinical characteristics"	"rna from unaffected colon biopsies. patients clinical characteristics"
Study Factor Type Term Accession Number	""	""
Study Factor Type Term Source REF	""	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-14442_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	""
Study Assay Measurement Type Term Source REF	""
Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE14442-3"	"P-GSE14442-7"	"P-GSE14442-4"	"P-GSE14442-5"	"P-GSE14442-6"	"P-GSE14442-2"	"P-GSE14442-1"
Study Protocol Type	"nucleic acid extraction protocol"	"nucleic acid extraction protocol"	"labeling protocol"	"hybridization protocol"	"array scanning protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"
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Study Protocol Description	"Total RNA was extracted from biopsies using the RNeasy Mini Kit (Qiagen, Westburg BV, The Netherlands) with on-column DNAse treatment (Qiagen). Needle homogenization was performed. The quality of RNA used for microarray analysis was checked on the Agilent 2100 Bioanalyzer (Agilent Technologies, Germany). Concentration and purity (ratio OD260/OD280 between 1.8 and 2.2) of the RNA used for quantitative real-time PCR was checked on a spectrophotometer (UV-1601, Shimadzu Benelux, Belgium)."	"extraction_protocol"	"A minimum of 5 µg total RNA was linearly amplified using in vitro transcription as described in detail in Puskás et al. (2002)."	"The probes were resuspended in 210µl hybridization solution containing 50% formamide, 1× HybridizationBuffer (cat# RPK0325; Amersham BioSciences), 0.1% SDS and 60µg/ml poly-dT. Hybridization and post-hybridization washing was performed at 45°C using an Automated Slide Processor (ASP) (Amersham BioSciences). Post-hybridization washing was performed in 1× SSC, 0.1% SDS, followed by 0.1× SSC, 0.1% SDS and 0.1× SSC."	"Arrays were scanned at 532 nm and 635 nm using a Generation III scanner (Amersham BioSciences, UK). Image analysis was performed with ArrayVision (Imaging Research Inc, Ontario, Canada)."	"Data were background corrected and each slide was normalized with a loess correction. The resulting base 2 corrected log-ratios (Cy5/Cy3) or (Cy3/Cy5) are reported here. ID_REF =  VALUE = Data were background corrected and each slide was normalized with a loess correction. The resulting base 2 corrected log-ratios (Cy5/Cy3) are reported here."	"Data were background corrected and each slide was normalized with a loess correction. The resulting base 2 corrected log-ratios (Cy5/Cy3) or (Cy3/Cy5) are reported here. ID_REF =  VALUE = Data were background corrected and each slide was normalized with a loess correction. The resulting base 2 corrected log-ratios (Cy3/Cy5) are reported here. INV_VALUE = Data were background corrected and each slide was normalized with a loess correction. The resulting base 2 corrected log-ratios (Cy5/Cy3) are reported here."
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STUDY CONTACTS
Study Person Last Name	"Allemeersch"	"Laukens"	"Van Hummelen"	"Rottiers"	"Remaut"	"De Vos"	"De Keyser"	"Peeters"	"Elewaut"
Study Person First Name	"Joke"	"Debby"	"Paul"	"Pieter"	"Erik"	"Martine"	"Filip"	"Harald"	"Dirk"
Study Person Mid Initials	""	""	""	""	""	""	""	""	""
Study Person Email	"joke.allemeersch@vib.be"	""	""	""	""	""	""	""	""
Study Person Phone	"+32(0)16 37 31 26"	""	""	""	""	""	""	""	""
Study Person Fax	"+32(0)16 37 31 29"	""	""	""	""	""	""	""	""
Study Person Address	"Nucleomics Core, Flanders Institute for Biotechnology (VIB), Herestraat 49 Box 816, Leuven, Belgium"	""	""	""	""	""	""	""	""
Study Person Affiliation	"Flanders Institute for Biotechnology (VIB)"	""	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""	""
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Comment[Study Person REF]	""	""	""	""	""	""	""	""	""