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Status |
Public on Mar 31, 2020 |
Title |
TM_rep2 |
Sample type |
SRA |
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|
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.
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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.
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|
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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
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|
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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 |