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Sample GSM3497456 Query DataSets for GSM3497456
Status Public on Mar 31, 2020
Title TM_rep2
Sample type SRA
 
Source name RNA from Salmonella grown in tomato medium
Organism Salmonella enterica
Characteristics serovar: Typhimurium
strain: 14028s
medium: tomato medium
Treatment protocol The minimal medium (MM) consisted of 20% M9 salts, 2 mM MgSO4 and 1.23 mM glucose in sterile deionized water. Tomato Medium (TM) and Lettuce medium (LM) contained 25% (v/v) plant extract and 20% M9 salts and 55% sterile deionized water. Plant root exudate media (LX, TX) consisted of lyophilized exudates (from about 25 plants, 4 h) resuspended in MgCl2. Soil suspensions consisted of 33% (v/v) soil in MgCl2.
Growth protocol Salmonella was grown overnight at 37°C in LB broth . The cells were pelleted at (1500 x g, 10 min), washed twice in 10 mM MgCl2 and OD600 = 1 was prepared. Two mL of this suspension were pipetted into dialysis tubes which were placed into 50 mL conical tubes containing 30 mL of minimal medium (MM). 2x 0.5 mL from each dialysis tube were mixed with RNAprotect then pelleted and the pelletes used for RNA extraction.
Extracted molecule total RNA
Extraction protocol The total RNA from the bacterial samples was extracted, the rRNA was removed and then the RNA was fragmented using the ultrasonicator.
The library preparation was done with the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing To reveal transcriptional differences in S. Typhimurium 14028s exposed to the different media Illumina HiSeq sequencing were performed at the ZIEL - Institute for Food & Health, Core Facility Microbiome/NGS, Technische Universität München, Freising, Germany.
The sequence analyses were mapped to NC_003197.2 whole genome using Bowtie2 v0.6 with parameters -s -p -x -U -s -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1 with cufflinks parameters -I 1 -F 0.0 -j 0.0 -G, cuffmerge parameters -g cuffdiff parameters -FDR 0.05 -c 10 -library-norm-method geometric -dispersion-method pooled
Genome_build: NC_003197.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each treatment, fold change and significance levels
 
Submission date Nov 29, 2018
Last update date Apr 01, 2020
Contact name Jasper Schierstaedt
E-mail(s) jasper.schierstaedt@julius-kuehn.de
Organization name Julius kühn-Institute
Department EP
Street address Messeweg 11-12
City Braunschweig
ZIP/Postal code 38104
Country Germany
 
Platform ID GPL19226
Series (1)
GSE132634 Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to tomato media
Relations
BioSample SAMN10502063
SRA SRX6183259
SRA SRX5081664

Supplementary file Size Download File type/resource
GSM3497456_Cuffq_TM2_Abund.cxb.gz 513.3 Kb (ftp)(http) CXB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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