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| Status |
Public on May 05, 2014 |
| Title |
rpoS_rep2 |
| Sample type |
SRA |
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| Source name |
Mutant rpoS double mutation 14028S
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| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain/background: 14028S
genotype: rpoS double mutation
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| Growth protocol |
Strains were grown aerobically to late stationary phase in rich medium (LB, 37°C, 200 rpm, 18h).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from Salmonella cells using TRIzol, digested with DNase I and the RNA quality was analyzed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Processed data file: GSE46380_S_Norel_statistics_WT-rpoSdb.xls
Processed data file: GSE46380_S_Norel_statistics_rpoSdb-deltarpoS.xls
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and for low-quality sequence using in-house program. Only sequence with a minimum length of 30 were considered, then mapped to 14028S whole genome sequence and plasmid (CP001363.1 and CP001362.1) using bowtie v0.12.7 with parameters --chunkmbs 200 -m 50 -e 59 -a --best --solexa1.3-quals
HTseq-count was used for counting genes with parameters -m -intersection-nonempty -s yes -t gene
Statistical analyses were performed using R version 2.15.1 and Bioconductor packages. Genes with nul raw counts in the nine samples were excluded from the data table. Normalisation and differential analysis were performed using DESeq version 1.8.3.
The whole dataset was first normalized using the normalization function of DESeq and dispersion was estimated with default parameters.
The statistical test was then applied on pairs of strains. Resulting p-values were adjusted for multiple comparisons according to the BH method. Two significance thresholds (0.05 and 0.001) were applied on adjusted p-values in order to declare genes as differentially expressed.
Genome_build: GenBank CP001363.1 and CP001362.1 (14028S).
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name, Salmonella typhimurium LT2 orthologs), Raw Counts (WT, Delta-rpoS, rpoSdb), Normalized Counts (WT, Delta-rpoS, rpoSdb), Statistics (rpoSdb/WT, Delta-rpoS/WT, Delta-rpoS/rpoSdb).
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| Submission date |
Apr 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Monot Marc |
| E-mail(s) |
mmonot@pasteur.fr
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| Phone |
+33145688390
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| Organization name |
Institut Pasteur
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| Department |
Genomes and Genetics
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| Lab |
Biomics
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| Street address |
25, rue du docteur roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL17070 |
| Series (1) |
| GSE46380 |
Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more? |
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| Relations |
| BioSample |
SAMN02056278 |
| SRA |
SRX271902 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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