ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"HP"	"EFO"	"BTO"	"NCBITAXON"	"XCO"	"DOID"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/HP"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/XCO"	"http://data.bioontology.org/ontologies/DOID"	
Term Source Version	"78"	"408"	"111"	"20"	"2"	"33"	"399"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Human Phenotype Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Experimental Conditions Ontology"	"Human Disease Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-46451"
Study Title	"Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies"
Study Description	"To seek effects of inflammatory status and 5-aminosalicylic acid (5-ASA, mesalazine) exposure ex vivo on mRNA levels within rectal mucosal biopsies from patients with ulcerative colitis. A total of 12 biopsies were analysed, 3 biological replicates in each of 4 categories (inflamed with or without 5-ASA, non-inflamed with or without 5-ASA)."
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2013-12-12"
Study File Name	"s_E-GEOD-46451_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
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STUDY FACTORS
Study Factor Name	"inflammation"	"compound"
Study Factor Type	"inflammation"	"compound"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-46451_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE46451-13"	"P-GSE46451-14"	"P-GSE46451-15"	"P-GSE46451-16"	"P-GSE46451-17"	"P-GSE46451-1"	"P-GSE46451-2"	"P-GSE46451-3"	"P-GSE46451-4"	"P-GSE46451-5"	"P-GSE46451-6"	"P-GSE46451-7"	"P-GSE46451-8"	"P-GSE46451-9"	"P-GSE46451-10"	"P-GSE46451-11"	"P-GSE46451-12"	"library construction"
Study Protocol Type	"sample treatment protocol"	"nucleic acid extraction protocol"	"labeling protocol"	"hybridization protocol"	"array scanning protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	"normalization data transformation protocol"	""
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Study Protocol Description	"Individual biopsies from areas of the rectum of patients with ulcerative colitis showing endoscopic signs of inflammation or not were placed luminal surface uppermost in a well of a 24-well tissue culture plate in 300µl of serum-free HL-1 chemically defined medium supplemented with 100 U/ml penicillin sodium, 100 mg/ml streptomycin sulphate, 50 �g/ml Gentamicin and cultured with or without 5-ASA (50mM) at 37°C, 95% air and 5% CO2 for 6h"	"RNAlater (Qiagen) then stored at -20°C until RNA extraction by RNeasy mini kits (Qiagen) and Dnase step"	"Ambion Total Prep 96"	"Standard Illumina protocol"	"Standard Illumina protocol"	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF no drug1.Avg_NBEADS =  INF no drug1.BEAD_STDERR =  INF no drug1.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF no drug2.Avg_NBEADS =  INF no drug2.BEAD_STDERR =  INF no drug2.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF no drug3.Avg_NBEADS =  INF no drug3.BEAD_STDERR =  INF no drug3.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF +5ASA1.Avg_NBEADS =  INF +5ASA1.BEAD_STDERR =  INF +5ASA1.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF +5ASA2.Avg_NBEADS =  INF +5ASA2.BEAD_STDERR =  INF +5ASA2.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] INF +5ASA3.Avg_NBEADS =  INF +5ASA3.BEAD_STDERR =  INF +5ASA3.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI no drug1.Avg_NBEADS =  NI no drug1.BEAD_STDERR =  NI no drug1.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI no drug2.Avg_NBEADS =  NI no drug2.BEAD_STDERR =  NI no drug2.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI no drug3.Avg_NBEADS =  NI no drug3.BEAD_STDERR =  NI no drug3.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI 5ASA1.Avg_NBEADS =  NI 5ASA1.BEAD_STDERR =  NI 5ASA1.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI 5ASA2.Avg_NBEADS =  NI 5ASA2.BEAD_STDERR =  NI 5ASA2.Detection Pval = "	"The data were normalized using Illumina's quantile normalization method (GenomeStudio software). ID_REF =  VALUE = Quantile-normalized signal [AVG_signal] NI 5ASA3.Avg_NBEADS =  NI 5ASA3.BEAD_STDERR =  NI 5ASA3.Detection Pval = "	""
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STUDY CONTACTS
Study Person Last Name	"Mein"	"MacFie"	"Boitsova"	"Nijhuis"	"Mein"	"Nuamah"	"Silver"	"Lindsay"
Study Person First Name	"Charles"	"Tammie"	"Tatjana"	"Anke"	"Charles"	"Rosamond"	"Andrew"	"James"
Study Person Mid Initials	""	"S"	""	""	"A"	"A"	"R"	"O"
Study Person Email	"c.a.mein@qmul.ac.uk"	""	""	""	""	""	""	""
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Study Person Address	"Genome Centre, Queen Mary University, Charterhouse Square, London, United Kingdom"	""	""	""	""	""	""	""
Study Person Affiliation	"Queen Mary University"	""	""	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""	""	""
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