ONTOLOGY SOURCE REFERENCE
Term Source Name	"NCBITAXON"	"OBI"	"BTO"	"UO"	"CHEBI"	"XCO"	"EFO"	
Term Source File	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/OBI"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/UO"	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/XCO"	"http://data.bioontology.org/ontologies/EFO"	
Term Source Version	"2"	"22"	"22"	"42"	"80"	"39"	"113"	
Term Source Description	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Ontology for Biomedical Investigations"	"BRENDA Tissue and Enzyme Source Ontology"	"Units of Measurement Ontology"	"Chemical Entities of Biological Interest Ontology"	"Experimental Conditions Ontology"	"Experimental Factor Ontology"	
INVESTIGATION
Investigation Identifier	"1411575658101"
Investigation Title	"Investigation"
Investigation Description	""
Investigation Submission Date	""
Investigation Public Release Date	""
Comment [Created with configuration]	""
Comment [Last Opened With Configuration]	""
Comment[Created With Configuration]	""
Comment[Last Opened With Configuration]	""
INVESTIGATION PUBLICATIONS
Investigation PubMed ID	""
Investigation Publication DOI	""
Investigation Publication Author List	""
Investigation Publication Title	""
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Investigation Publication Status Term Accession Number	""
Investigation Publication Status Term Source REF	""
INVESTIGATION CONTACTS
Investigation Person Last Name	""
Investigation Person First Name	""
Investigation Person Mid Initials	""
Investigation Person Email	""
Investigation Person Phone	""
Investigation Person Fax	""
Investigation Person Address	""
Investigation Person Affiliation	""
Investigation Person Roles	""
Investigation Person Roles Term Accession Number	""
Investigation Person Roles Term Source REF	""
STUDY
Study Identifier	"1_jhlab-rnaseq1"
Study Title	"HT-Seq profiling of HASMCs treated with NSAIDS and induced with IL-1B"
Study Description	"The goal of this experiment is to identify differences in gene expression in Human Aorta Smooth Muscle cells (HASMCs) treated with the selective and non-selective COX2 inhibitors, celecoxib and naproxen, respectively. HASMCs were treated with various doses of naproxen/celecoxib for 3hrs and then induced with the inflammatory stimuli IL-1B for 0, 2 or 8hrs (extraction time points). At each extraction time point, an aliquot of the media was stored and cells were lysed and stored in TRIZol reagent. The TRIZol reagent was later processed for total RNA extraction."
Study Submission Date	""
Study Public Release Date	""
Study File Name	"s_AOG-hasmc-CeleNapr.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"time series design"	"compound treatment design"	"stimulus or stress design"	"dose response design"
Study Design Type Term Accession Number	"http://www.ebi.ac.uk/efo/EFO_0001779"	"http://www.ebi.ac.uk/efo/EFO_0001755"	"http://www.ebi.ac.uk/efo/EFO_0001762"	"http://www.ebi.ac.uk/efo/EFO_0001757"
Study Design Type Term Source REF	"EFO"	"EFO"	"EFO"	"EFO"
STUDY PUBLICATIONS
Study PubMed ID	""
Study Publication DOI	""
Study Publication Author List	""
Study Publication Title	""
Study Publication Status	""
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"NSAID"	"NSAID concentration"	"IL-1beta exposure"
Study Factor Type	"drug"	"dose"	"time"
Study Factor Type Term Accession Number	"http://purl.obolibrary.org/obo/CHEBI_23888"	"http://www.ebi.ac.uk/efo/EFO_0000428"	"http://www.ebi.ac.uk/efo/EFO_0000721"
Study Factor Type Term Source REF	"EFO"	"EFO"	"EFO"
STUDY ASSAYS
Study Assay File Name	"a_aog-hasmc-celenapr_transcription_profiling_nucleotide_sequencing.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	"obo:OBI_0000424"
Study Assay Measurement Type Term Source REF	"OBI"
Study Assay Technology Type	"nucleotide sequencing"
Study Assay Technology Type Term Accession Number	"obo:OBI_0000626"
Study Assay Technology Type Term Source REF	"OBI"
Study Assay Technology Platform	"Illumina"
STUDY PROTOCOLS
Study Protocol Name	"growth protocol"	"treatment protocol"	"Sample collection"	"nucleic acid extraction protocol"	"nucleic acid library construction protocol"	"pooling protocol"	"nucleic acid sequencing protocol"	"sequence analysis data transformation"	"normalization data transformation protocol"	"combine files"
Study Protocol Type	"growth protocol"	"treatment protocol"	"cell collecting"	"nucleic acid extraction protocol"	"nucleic acid library construction protocol"	"sample pooling"	"nucleic acid sequencing protocol"	"sequence analysis data transformation"	"normalization data transformation protocol"	"data transformation"
Study Protocol Type Term Accession Number	"http://www.ebi.ac.uk/efo/EFO_0003789"	"http://www.ebi.ac.uk/efo/EFO_0003969"	"http://purl.obolibrary.org/obo/OBI_0001483"	"http://www.ebi.ac.uk/efo/EFO_0002944"	"http://www.ebi.ac.uk/efo/EFO_0004184"	"http://www.ebi.ac.uk/efo/EFO_0005316"	"http://www.ebi.ac.uk/efo/EFO_0004170"	"http://purl.obolibrary.org/obo/OBI_0200187"	"http://www.ebi.ac.uk/efo/EFO_0003816"	"http://purl.obolibrary.org/obo/OBI_0200000"
Study Protocol Type Term Source REF	"EFO"	"EFO"	"OBI"	"EFO"	"EFO"	"EFO"	"EFO"	"OBI"	"EFO"	"EFO"
Study Protocol Description	"Primary human aortic smooth muscle cells (Caucasian donor, age and weight unknown) were routinely passaged in Smooth muscle basal medium (CC-3182, Lonza) supplemented with the SMGM-2-bulletkit (CC-3181, Lonza) according to suppliers instructions."	"Cells were serum starved overnight and then treated with celecoxib or naproxen. DMSO/H20 (final 0.84 DMSO/100 ul) were added to naproxen and celecoxib mastermixes to account for vehicles used in stock. Three hours later, cells were treated with IL-1B (1 ng/mL) for 0, 2 or 8 hours. Generally, the experiment started in the morning and ended in the evening."	"At each IL-1B exposure time, 1 mL of media was extracted and stored at -80C and the rest of the media was aspirated. Trizol was immediately added to each tube.  Samples were stored at -80C to processing."	"The samples were all extracted in the same run using the Direct-zol-96 RNA kit (ZYMO research, cat # R2054) according the manufacturers protocol.  All samples were eluted in 50uL of RNase free water. QC was carried out using an Agilent Bioanalyzer 2100 Eukaryote Total RNA Nano."	"RNA libraries were prepared with the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to manufacturer's instructions. The Illumina predicted library size was 260 bp. Library fragment size was measured on a LabChip GX (Caliper Life Sciences)."	"Six samples were pooled per lane."	"Sequencing was carried out on an Illumina HiSeq 2000 at the Children's Hospital of Philadelphia High-Throughput Sequencing Center BGI@CHOP."	"Reads were aligned to hg19 using STAR-2.3.0e with the following flags: 

runThreadN 10
outSAMstrandField intronMotif 
runMode alignReads
outFileNamePrefix star/
genomeDir ~/index/hg19
readFilesCommand zcat
readFilesIn SAMPLE_NAME_1.fq.gz SAMPLE_NAME_2.fq.gz

SAM files were converted to BAM format and sorted using SAMTools."	""	"Declustering was carried out by BGI@CHOP. One fastq file with the forward reads and one fastq file with the reverse reads was created."
Study Protocol URI	""	""	""	""	""	""	""	""	""	""
Study Protocol Version	""	""	""	""	""	""	""	""	""	""
Study Protocol Parameters Name	""	"NSAID;vehicle;duration of dosing;dose"	""	""	"selection strategy;library facility;libprep_day2;libprep_day1;mid;kit;PCR cycles;library layout"	""	"read length;sequencing instrument;demultiplex;base caller;quality score;facility"	"alignment algorithm"	""	""
Study Protocol Parameters Name Term Accession Number	""	";;;"	""	""	";;;;;;;"	""	";;;;;"	""	""	""
Study Protocol Parameters Name Term Source REF	""	";;;"	""	""	";;;;;;;"	""	";;;;;"	""	""	""
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Comment[Is Private Protocol]	""	""	""	""	""	""	""	""	""	""
STUDY CONTACTS
Study Person Last Name	"Hogenesch"	"Olarerin-George"	"Francey"	"Growe"
Study Person First Name	"John"	"Anthony"	"Lauren"	"Jacki"
Study Person Mid Initials	"B"	""	""	""
Study Person Email	"hogenesc@mail.med.upenn.edu"	"olarerin@mail.med.upenn.edu"	"franceyl@mail.med.upenn.edu"	""
Study Person Phone	""	""	""	""
Study Person Fax	""	""	""	""
Study Person Address	""	""	""	""
Study Person Affiliation	"University of Pennsylvania"	"University of Pennsylvania"	"University of Pennsylvania"	"University of Pennsylvania"
Study Person Roles	""	""	""	""
Study Person Roles Term Accession Number	""	""	""	""
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Comment[Lab]	""	""	""	""