ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"XCO"	"UO"	"UBERON"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/XCO"	"http://data.bioontology.org/ontologies/UO"	"http://data.bioontology.org/ontologies/UBERON"	
Term Source Version	"78"	"111"	"33"	"42"	"191"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"Experimental Conditions Ontology"	"Units of Measurement Ontology"	"Uber Anatomy Ontology"	
INVESTIGATION
Investigation Identifier	"1400600658390"
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-38151"
Study Title	"Xenobiotics shape the physiology and gene expression of the active human gut microbiome"
Study Description	"RNA-Seq transcriptional profiling of human gut metagenome after several days of incubation in the presence of various drugs. [original description: The human gut is colonized by trillions of microorganisms that influence human health and disease through the metabolism of xenobiotics, including therapeutic drugs and antibiotics. The diversity and metabolic potential of the human gut microbiome have been extensively characterized, but it remains unclear which microorganisms are active and which perturbations can influence this activity. Here, we use flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the human gut contains distinctive subsets of active and damaged microorganisms, primarily composed of Firmicutes, which display marked temporal variation. Short-term exposure to a panel of xenobiotics resulted in significant changes in the physiology and gene expression of this active microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding novel candidate proteins for antibiotic resistance, drug metabolism, and stress response. These results demonstrate the power of moving beyond DNA-based measurements of microbial communities to better understand their physiology and metabolism. RNA-Seq analysis of the human gut microbiome during exposure to antibiotics and therapeutic drugs.]"
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Study Public Release Date	"2012-10-30"
Study File Name	"s_E-GEOD-38151_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"RNA-seq of coding RNA"
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STUDY PUBLICATIONS
Study PubMed ID	"23332745"
Study Publication DOI	"10.1016/j.cell.2012.10.052"
Study Publication Author List	"Maurice CF, Haiser HJ, Turnbaugh PJ"
Study Publication Title	"Xenobiotics shape the physiology and gene expression of the active human gut microbiome."
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STUDY FACTORS
Study Factor Name	"incubation time"	"treatment protocol of gut microbiome"	"collection day"	"healthy adult"
Study Factor Type	"incubation time"	"treatment protocol of gut microbiome"	"collection day"	"healthy adult"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-38151_RNA-Seq_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"nucleotide sequencing"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE38151-2"	"P-GSE38151-1"	"P-GSE38151-3"	"library construction"	"nucleic acid sequencing"	"P-GSE38151-4"
Study Protocol Type	"growth protocol"	"sample treatment protocol"	"nucleic acid library construction protocol"	"library construction"	"nucleic acid sequencing"	"normalization data transformation protocol"
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Study Protocol Description	"Unless specified otherwise all incubations took place for 4 hours under anaerobic conditions, in the dark, and at 37�C. Fresh fecal samples from three unrelated healthy adults were diluted 1:10 (w/vol) in freshly prepared BHI (pH7; Becton Dickinson) liquid medium."	"In total, we tested six therapeutic drugs and eight antibiotics (10μg/ml final concentration), in addition to low pH and mutiple controls."	"Microbial cells from samples before and after the 4-hour incubations were lysed by a bead beater (BioSpec Products), total RNA was extracted with phenol:chloroform:isoamyl alcohol (pH 4.5, 125:24:1, Ambion 9720), purified using MEGAClear columns (Ambion), and rRNA was depleted via subtractive hybridization (MICROBExpress, Ambion, in addition to custom depletion oligos). The presence of genomic DNA contamination was assessed by PCR with universal 16S rDNA primers. cDNA was synthesized using SuperScript II and random hexamers (Invitrogen), followed by second strand synthesis with RNaseH and E.coli DNA polymerase (New England Biolabs). Samples were prepared for sequencing with an Illumina Hi-Seq instrument after enzymatic fragmentation (NEBE6040L/M0348S). Libraries were quantified by quantitative reverse transcriptase PCR (qRT-PCR) according to the Illumina protocol. qRT-PCR assays are run using ABsoluteTM QPCR SYBR Green ROX Mix (Thermo Scientific) on a Mx3000P QPCR System instrument (Stratagene, La Jolla, CA). The size distribution of each library was quantified on an Agilent HS-DNA chip."	""	""	"Pre-processing of raw reads: trimmed ends to min score = 20 and minimum length = 20, required both pairs, concatenated each trimmed pair Mapped reads to 539 human-associated genomes (http://www.hmpdacc.org/) using SSAHA (version 2; parameters: -best 1 -score 20 -solexa) The number of transcripts assigned to each gene was then tallied. Supplementary_files_format_and_content: Counts files were generated. Values are total reads assigned and fraction reads assigned (#reads/total reads) [columns 2 and 3, respectively]."
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STUDY CONTACTS
Study Person Last Name	"Turnbaugh"	"Maurice"	"Haiser"	"Turnbaugh"
Study Person First Name	"Peter"	"Corinne"	"Henry"	"Peter"
Study Person Mid Initials	"James"	"F"	"J"	"J"
Study Person Email	"pturnbaugh@fas.harvard.edu"	""	""	""
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Study Person Address	"Center for Systems Biology, Harvard University, 52 Oxford St Room 435.40, Cambridge, MA, USA"	""	""	""
Study Person Affiliation	"Harvard University"	""	""	""
Study Person Roles	"submitter"	""	""	""
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