ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"BTO"	"EFO"	"NCBITAXON"	"NCIT"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/NCIT"	
Term Source Version	"78"	"20"	"111"	"2"	"24"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Experimental Factor Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"National Cancer Institute Thesaurus"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-2950"
Study Title	"Transcriptional profiling of mouse ears exposed to the irritant sulfur mustard with or without drug (including indomethacin) pre-treatment. [original title: Transcription profiling of mouse ears exposed to sulfur mustard alone, sulfur mustard preceded by drug treatment, or vehicle compounds to identify gene expression changes that correlate with compound efficacy]"
Study Description	"Sulfur mustard (SM) is a potent alkylating agent. We are developing medical countermeasures to reduce the injury caused by SM exposure. Screening in the mouse ear vesicant model has identified three effective compounds: dimercaprol (British anti-lewisite), indomethacin, and octyl homovanillamide (OHV). To identify gene expression changes that correlate with compound efficacy we used oligonucleotide microarrays to compare gene expression profiles in vehicle-exposed skin, SM-exposed skin, and skin pretreated with each compound before SM exposure. Mice were topically exposed on the inner surface of the right ear to SM alone or pretreated for 15 min with one of the compounds and then exposed to SM. Left ears were vehicle-exposed. Ear tissue was harvested 24 hr later for ear weight determination (an endpoint indicating compound efficacy). The exposure groups were: methylene chloride (sulfur mustard vehicle); ethanol (drug vehicle); 0.08 mg sulfur mustard; 6.25 mg dimercaprol 15 min before 0.08 mg sulfur mustard; 1.34 mg indomethacin 15 min before 0.08 mg sulfur mustard; 0.6 mg octylhomovanillamide 15 min before 0.08 mg sulfur mustard; 6.25 mg dimercaprol alone; 1.34 mg indomethacin alone; 0.6 mg octylhomovanillamide alone. RNA was extracted from the tissues and used to generate oligonucleotide microarray probes. Principal component analysis of the gene expression data revealed partitioning of the samples based on drug treatment and SM exposure. Vehicle-exposed mouse ears clustered away from the other treatment groups. SM-exposed mouse ears pretreated with dimercaprol or OHV clustered more closely with vehicle-exposed ears, while SM-exposed mouse ears pretreated with indomethacin clustered more closely with SM-exposed ears. This clustering of the samples is supported by the ear weight data, in which the indomethacin group has ear weights closer to the SM-exposed group, whereas the dimercaprol and OHV groups have ear weights closer to the vehicle-exposed group. Correlation coefficients were calculated for each gene based on the correlation between gene expression level and ear weight. These data provide the basis for understanding what gene expression changes are important in the development of effective SM medical countermeasures. Experiment Overall Design: Exposure of mouse ears to sulfur mustard alone, sulfur mustard preceded by drug treatment, or vehicle compounds. Naive controls were also included. Biological replicates of at least n=3 were examined for each exposure condition."
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Study Public Release Date	"2007-12-01"
Study File Name	"s_E-GEOD-2950_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"compound_treatment_design"	"co-expression_design"	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"16377760"
Study Publication DOI	"16377760"
Study Publication Author List	"James F Dillman, Alison I Hege, Christopher S Phillips, Linda D Orzolek, Albert J Sylvester, Carol Bossone, Claudia Henemyre-Harris, Robyn C Kiser, Young W Choi, John J Schlager, Carol L Sabourin"
Study Publication Title	"Microarray analysis of mouse ear tissue exposed to bis-(2-chloroethyl) sulfide: gene expression profiles correlate with treatment efficacy and an established clinical endpoint."
Study Publication Status	"journal_article"
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STUDY FACTORS
Study Factor Name	"compound"	"organismpart"
Study Factor Type	"compound"	"organism_part"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-2950_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-G2950-6"	"P-G2950-2"	"P-G2950-3"	"P-G2950-4"	"P-G2950-5"
Study Protocol Type	"grow"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"
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Study Protocol Description	"A single 5 microL application of SM (0.08 mg dose, 0.5 micromoles) in methylene chloride was applied topically to the inner surface of the right ear.  The left ear (vehicle control) was exposed to 5 microL of methylene chloride only.  For drug treatment, animals were administered 10 microL of dimercaprol (6.25 mg dose, 50.3 micromoles), 30 microL of OHV (0.585 mg dose, 1.995 micromoles), or 20 microL of indomethacin (1.34 mg dose, 3.74 micromoles) in ethanol 15 minutes prior to SM challenge.  A group of animals received only drug on the right ear and ethanol (drug vehicle) on the left ear.  A group of untreated, unexposed animals served as naive controls.  At 24 hr post-exposure, animals were euthanized and an 8 mm diameter skin biopsy was obtained.  The skin biopsy was weighed and immediately frozen in liquid nitrogen."	"RNA was isolated from frozen mouse ear biopsies using the RNeasy Mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.  The quality and amount of RNA was monitored throughout processing with an Agilent Bioanalyzer (Agilent, Palo Alto, CA) and a NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop Technologies, Rockland, DE)."	"10 ug of total RNA was used to generate first-strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with biotinylated nucleotides (Enzo Kits from Affymetrix), resulting in approximately 100-fold amplification of cRNA.  The target cRNA generated from each sample was processed as per manufacturer's recommendation using an Affymetrix GeneChip Instrument System (http://www.affymetrix.com/support/technical/ manual/expression_manual.affx)."	"Spiked controls were added to 15 µg of fragmented cRNA before overnight hybridization using 10 µg of cRNA."	"Arrays were washed and stained with streptavidin-phycoerythrin before being scanned on an Agilent GeneArray Scanner driven by Microarray Suite 5.0 software (Affymetrix).  After scanning, array images were assessed by eye to confirm scanner alignment and the absence of significant bubbles or scratches on the chip surface."
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STUDY CONTACTS
Study Person Last Name	"Dillman"
Study Person First Name	"James"
Study Person Mid Initials	"F."
Study Person Email	"james.dillman@apg.amedd.army.mil"
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Study Person Address	"Molecular Toxicology Team, Cell and Molecular Biology Branch, U.S. Army Medical Research Institute of Chemical Defense, 3100 Ricketts Point Rd, Aberdeen Proving Ground, 21010-5400, USA"
Study Person Affiliation	"U.S. Army Medical Research Institute of Chemical Defense"
Study Person Roles	"submitter"
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