Comment[ArrayExpressAccession]	E-GEOD-45445
MAGE-TAB Version	1.1			
Public Release Date	2013-03-26
Investigation Title	RNA-seq analysis of Salmonella enterica Typhimurium LT2			
Comment[Submitted Name]	RNA-seq analysis of Salmonella enterica Typhimurium LT2
Experiment Description	We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during  glucose-phosphate stress.  In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response. Wild-type Salmonella cells, mutants of Salmonella either lacking sgrS or  lacking SgrS RNA/ SgrT peptide function were subject to glucose-phoshate stress			
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	Tjaden	Balasubramanian	Vanderpool	
Person First Name	Brian	Divya	Carin	
Person Mid Initials			K	
Person Email	geo@ncbi.nlm.nih.gov			
Person Affiliation	Wellesley College			
Person Address	Wellesley College, 106 Central Street, Wellesley, MA, USA			
Person Roles	submitter			
Protocol Name	P-GSE45445-1	P-GSE45445-3	P-GSE45445-2	P-GSE45445-4
Protocol Description	Each of the mutant strains above were grown in min. Mops fructose medium until cultures reached an OD600 of ~0.3. Cultures were then treated with the glucose-analog alpha-methyl glucoside (αMG), and total RNA harvested 15' after treatment	Hot phenol RNA extraction as described in Aiba. Adhya and Crombrugghe. J. Bio Chem. 1981, 256: p. 11905-11910. Ribosomal RNA was first removed using the Ribozero rRNA Removal Meta-Bacteria kit. Enriched mRNAs were then converted into indexed libraries using the into ScriptSeqTM v2 RNA-Seq Library Preparation Kit	Minimal mops medium , carbon source: fructose	Rockhopper version 1.20 (manuscript submitted) was used for alignment, normalization, and quantification. Rockhopper is available for download from http://cs.wellesley.edu/~btjaden/Rockhopper Genome_build: Salmonella enterica subsp. Enterica serovar Typhimurium st. LT2 (NC_003197.1)/ASM694v1 Supplementary_files_format_and_content: Tab delimited text files containing transcription coordinates and abundance estimates.
Protocol Type	specified_biomaterial_action	nucleic acid library construction protocol	grow	feature_extraction
Experimental Factor Name	TREATMENT	GENOTYPE		
Experimental Factor Type	treatment	genotype		
Comment[SecondaryAccession]	GSE45445			
Comment[GEOReleaseDate]	2013-03-26			
Comment[ArrayExpressSubmissionDate]	2013-03-23			
Comment[GEOLastUpdateDate]	2013-03-26			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AdditionalFile:Data1]	GSE45445_Operons.txt			
Comment[AdditionalFile:Data2]	GSE45445_Summary.txt			
Comment[AdditionalFile:Data3]	GSE45445_Transcripts.txt			
Comment[SecondaryAccession]	SRP019960			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR794912-SRR794919			
SDRF File	E-GEOD-45445.sdrf.txt