|
| Status |
Public on Mar 08, 2016 |
| Title |
plasma-t4_3 |
| Sample type |
RNA |
| |
|
| Source name |
Staphylococcus aureus cells
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: HG001
genotype: wild type
treatment: growth in human plasma 4h stationary phase
|
| Treatment protocol |
Detailed treatment protocols can be found in the Supplementary Online Material (Mäder, Nicolas et al., to be submitted)
|
| Growth protocol |
S. aureus HG001 was grown under different conditions including different growth media, presence of sub-inhibitory concentrations of antibiotics, anaerobic growth conditions, and internalization in eukaryotic host cells.
The complete description of the growth protocols can be found in the Supplementary Online Material (Mäder, Nicolas et al., to be submitted).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as described previously (Nicolas et al., 2012, Science 335, 1103-1106). The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009, Mol Microbiol 73, 1043-1057).
|
| |
|
| Hybridization protocol |
Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.
|
| Description |
growth in human plasma_4h stationary phase_replicate 3
|
| Data processing |
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in Nicolas et al., 2009, Bioinformatics 25, 2341-2347.
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008, Nucl Acids Res 36, 2926-2938).
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
Mar 09, 2016 |
| Contact name |
Pierre Nicolas |
| E-mail(s) |
pierre.nicolas@inrae.fr
|
| Phone |
+33-1-3465-2894
|
| Organization name |
INRAE - Université Paris-Saclay
|
| Lab |
MaIAGE
|
| Street address |
INRAE - Domaine de Vilvert
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
F-78350 |
| Country |
France |
| |
|
| Platform ID |
GPL20586 |
| Series (2) |
| GSE70040 |
Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions |
| GSE70043 |
Staphylococcus aureus HG001 |
|
