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| Status |
Public on Jun 16, 2018 |
| Title |
dR3 |
| Sample type |
SRA |
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| Source name |
Staphylococcus aureus HG003
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| Organism |
Staphylococcus aureus |
| Characteristics |
strain: {delta}rsaE
induction: --
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| Growth protocol |
Overnight cultures were diluted 1000 times and incubated in BHI at 37°C. For HG003 and HG003 ΔrsaE, strains were harvested at OD600 6. For HG003 ΔrsaE pRMC2RsaE, at OD600 0.5, the culture was split in two halves and anhydrotetracycline (aTc, 1 mM) was added to one of them. Induced and non-induced cultures were harvested 5 min after aTc addition.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted as described (Bohn, C., Rigoulay, C. and Bouloc, P. 2007. BMC Microbiol, 7, 10). Samples were treated with TURBO DNase (Ambion) according to manufacturer’s instructions. Ten µg of RNA were depleted for ribosomal RNA with MICROBExpress (Ambion).
Strand-specific RNA-seq libraries were generated with the TruSeq SBS Kit v3 (Illumina), according to the manufacturer's instructions.
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| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Description |
processed data file: Supplemental_table_1.txt
test condition replicat 3 (transcriptome comparison: ΔrsaE relative to wild-type)
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| Data processing |
FastQC (v0.10.1) quality control.
Mapping performed on Refseq CP000253.1 with bowtie2 (v2.1.0) using default values.
The raw counts of the number of uniquely mapped reads to each CDS described in Refseq CP000253.1 were done with featureCounts (1.5.0-p1, with the options of both paired-end reads and stranded library) [Liao, 2014].
Differential expression analyzes (normalisation and statistical tests) were performed using the SARTools with DESeq2 software (Varet, Brillet-Gueguen et al. 2016) using two conditions (rsaE mutant relative to wild-type, and 5 min induced relative to non-induced RsaE expression). Genes with a BH-adjusted p-value < 0.05 and a fold change > 1.33 were considered as differentially expressed.
Genome_build: CP000253.1
Supplementary_files_format_and_content: Supplemental_table_1: Full results of the DEseq2 analysis "rsaE mutant relative to wild-type" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; StrainReplicat= raw counts for 'StrainReplicat' sample ('strain' and 'replicat' take the possible values 'WT' for wild-type, 'dR' for rsaE mutant, '1' and '3' resp.); norm.StrainReplicat = Rounded normalized counts for 'StrainReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.
Supplementary_files_format_and_content: Supplemental_table_2: Full results of the DEseq2 analysis "Induced relative to non-induced RsaE expression" for all CDS. Column legends : Id=Accession number retrieved from Refseq CP000253.1 ; InductionReplicat= raw counts for 'InductionReplicat' sample ('Induction' and 'Replicat' take the possible values 'dRT0' for non-induced, 'dRT5' for induced, and '1', '2' and '3' are for triplicates, resp.); norm.InductionReplicat = Rounded normalized counts for 'InductionReplicat' sample; baseMean=Base mean over all samples ; FoldChange=Fold change of expression, calculated as 2log2(FC) ; log2FoldChange=Log2(FC) as estimated by the GLM model. pvalue=Raw p-value from the statistical test ; dispGeneEst=dispersion parameter estimated from feature counts ; dispFit=dispersion parameter estimated from the model ; dispMAP=dispersion parameter estimated from the Maximum A Posteriori model ; dispersion=final dispersion parameter used to perform the test ; betaConv=convergence of the coefficients of the model (TRUE or FALSE) ; maxCooks=maximum Cook's distance of the feature.
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| Submission date |
Nov 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tatiana Rochat |
| E-mail(s) |
tatiana.rochat@jouy.inra.fr
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| Organization name |
INRA
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| Lab |
Virologie et Immunologie Moléculaires
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| Street address |
Domaine de Vilvert
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| City |
Jouy-en-Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
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| Platform ID |
GPL24214 |
| Series (2) |
| GSE106456 |
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq] |
| GSE106457 |
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus |
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| Relations |
| BioSample |
SAMN07967427 |
| SRA |
SRX3353473 |
| 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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