Comment[ArrayExpressAccession]	E-GEOD-43893
MAGE-TAB Version	1.1		
Public Release Date	2013-10-22
Investigation Title	RNA sequencing of SHP -/- knockout mouse transcriptome		
Comment[Submitted Name]	RNA sequencing of SHP -/- knockout mouse transcriptome
Experiment Description	Goal of this study is to identify annotated and non-annotated genes transcriptionally regulated by small heterodime partner (SHP, Nrob2) expression. Liver 5' capped RNA samples from three SHP -/- and three wild type mice were sequenced with Illumina GAII sequencer.		
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl	
Person Last Name	Delker	Wang	Hagedorn
Person First Name	Don	Li	Curt
Person Email	don.delker@hsc.utah.edu		
Person Affiliation	University of Utah		
Person Address	School of Medicine, University of Utah, 30 North 1900 East, Salt Lake City, Utah, USA		
Person Roles	submitter		
Protocol Name	P-GSE43893-2	P-GSE43893-1	
Protocol Description	36 cycle paired end reads (fastq files) were aligned to mouse July 2007 (NCBI37/mm9) genome with novoalign version 2.05.33 software Novoaligned sam files were parsed into binary point data files with Useq version 6.2 software. Differential gene expression was determined using Useq MultipleReplicaDefinedRegionScanSeqs (MRDRSS) application to count reads intersecting exons of each annotated gene. Sequencing reads for each sample were normalized using reads per kilobase gene length per million reads (RPKM). Genome_build: mm9 Supplementary_files_format_and_content: Single text file containing raw read counts for each sample, average normalized read counts for each mouse genotype, log2 ratio, negative binomial p-value and false discovery rate of SHP -/- to wild type comparison.	Total RNA extracted with TriZOL, then 5' capped RNA selected with high affinity EIF4E variant (Choi and Hagedorn, 2003, PNAS 100:7033-7038) Standard Illumina library protocol for barcoding samples. Three barcoded samples were sequenced per lane. 36 cycle paired end reads were generated for each sample.	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	
Experimental Factor Name	GENOTYPE/VARATION		
Experimental Factor Type	genotype/varation		
Publication Title	Genome-wide transcriptome analysis identifies novel gene signatures implicated in human chronic liver disease.		
Publication Author List	Smalling RL, Delker DA, Zhang Y, Nieto N, McGuiness MS, Liu S, Friedman SL, Hagedorn CH, Wang L		
PubMed ID	23812039		
Publication DOI	10.1152/ajpgi.00077.2013		
Comment[SecondaryAccession]	GSE43893		
Comment[GEOReleaseDate]	2013-10-22		
Comment[ArrayExpressSubmissionDate]	2013-01-30		
Comment[GEOLastUpdateDate]	2013-11-12		
Comment[AEExperimentType]	RNA-seq of coding RNA		
Comment[AdditionalFile:Data1]	GSE43893_SHP_RNA-Seq_Processed.txt		
Comment[SecondaryAccession]	SRP018291		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR653850-SRR653855		
SDRF File	E-GEOD-43893.sdrf.txt