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Sample GSM3392015 Query DataSets for GSM3392015
Status Public on Sep 18, 2018
Title STM_plus_1
Sample type SRA
 
Source name bacterial culture
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics genetic background: ∆ssrAB
plasmid: pWSK129-PssrA-ssrB D56E
Growth protocol Overnight bacterial cultures were sub-cultured 1:50 in LB-kanamycin and grown at shaking for 2.5 hours. These were then sub-cultured 1:50 into LPM pH 5.8 and grown to mid log (OD600=0.4-0.5). Bacteria were then pelleted by centrifugation for RNA extraction.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol-chloroform separation, precipitated with isopropanol, washed with 75% ethanol, resuspended in water for Dnase I treatment for 30 min. Dnase I was inactivated with inactivation beads and RNA was re-precipitated with isopropanol, washed with 75% ethanol, and resuspended in water
RNA was rRNA depleted with RiboZero, and strand specific dUTP sequencing was performed on an Illumina Hi-Seq following standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description processed data file: NC_016810_transcripts.txt
processed data file: NC_017718_transcripts.txt
processed data file: NC_017719_transcripts.txt
processed data file: NC_017720_transcripts.txt
Data processing Multiple files for each sample were concatenated into a single file. SsrB- and SsrB+ files for each species were loaded on to Rockhopper for alignment to the referene genome and plasmids if applicable.
Genome_build: Reference genome for S. bongori NC_015761. Reference genome for S. Typhimurium NC_016810. Reference for S. Typhimurium plasmids NC_017718 (pCol1B9), NC_017719 (pRSF), NC_017720 (pSLT)
Reads were mapped to the respective genomes with Rockhopper and differential gene expression (SsrB+/SsrB-) was calculated for both species.
 
Submission date Sep 17, 2018
Last update date Sep 18, 2018
Contact name Brian Coombes
E-mail(s) coombes@mcmaster.ca
Phone 905 525 9140
Organization name McMaster University
Department Biochemistry and Biomedical Sciences
Street address MDCL 2108. 1200 Main St W, McMaster University
City Hamilton
State/province ON
ZIP/Postal code L8N 4L8
Country Canada
 
Platform ID GPL17070
Series (1)
GSE120043 RNA-sequencing of SsrB-dependent gene expression in S. Typhimurium and S. bongori
Relations
BioSample SAMN10077654
SRA SRX4702830

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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