Comment[ArrayExpressAccession]	E-GEOD-45316
MAGE-TAB Version	1.1				
Public Release Date	2013-03-21
Investigation Title	Transcript structures in Shewanella loihica PV-4				
Comment[Submitted Name]	Transcript structures in Shewanella loihica PV-4
Experiment Description	5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.				
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	Shao	Shao	Price	Deutschbauer	Arkin
Person First Name	Wenjun	Wenjun	Morgan	Adam	Adam
Person Mid Initials			N	M	P
Person Email	wshao@lbl.gov				
Person Affiliation	University of California				
Person Address	Molecular and Cell Biology, University of California, 2151 Berkeley Way, Berkeley, CA, USA				
Person Roles	submitter				
Protocol Name	P-GSE45316-2	P-GSE45316-1	P-GSE45316-3		
Protocol Description	Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes. Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment. RNA quality was confirmed with an Agilent Bioanalyze. Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA. We used terminator 5'-P-dependent exonuclease to degrade transcripts with non-triphosphate 5' ends, TAP phosphatase to convert 5'-PPP to 5'-P ends, blocked the 3' ends with sodium periodate and we added a sequencing adaptor onto the 5' end with Ambion T4 RNA ligase. We used random hexamer primers with a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR amplified the library to enrich for products that contained both adaptors and to complete the 5' adaptor. 6-mer index GTGGCC was incorporated into the reverse PCR primer. We purified the PCR products and removed unincorporated nucleotides, primers, and adaptor-only products with AMPure XP Beads (Agencourt).	Aerobic growth to mid-log phase at 30C with shaking at 200 rpm	Basecalls performed using Illumina CASAVA_v1.8.0 Filter out the reads that did not pass the quality filter by Illumina CASAVA 1.8 Sequenced reads were trimmed for adaptor sequence, then mapped to Shewanella loihica PV-4 genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1 Peaks were called by counting the total number of reads whose starts mapped to the genome location Genome_build: Shewanella loihica PV-4/ASM1606v1 Supplementary_files_format_and_content: wig file per sample per scaffold per strand		
Protocol Type	nucleic acid library construction protocol	grow	feature_extraction		
Experimental Factor Name	TREATMENT				
Experimental Factor Type	treatment				
Comment[SecondaryAccession]	GSE45316				
Comment[GEOReleaseDate]	2013-03-21				
Comment[ArrayExpressSubmissionDate]	2013-03-19				
Comment[GEOLastUpdateDate]	2013-03-22				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[SecondaryAccession]	SRP019795				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR786960-SRR786961				
SDRF File	E-GEOD-45316.sdrf.txt