|
| Status |
Public on Mar 07, 2012 |
| Title |
Salt_1 |
| Sample type |
RNA |
| |
|
| Source name |
Bacillus subtilis cells
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
strain: 168
condition: growth in SMM medium until OD500 of 0.4 10 minutes after addition of 0.4 M NaCl
replicate: 1
|
| Treatment protocol |
The study comprised adaptation to stresses such as treatment with oxidative agents, nutrient starvation, temperature and osmotic variations.
Detailed treatment protocols are available in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted)
|
| Growth protocol |
The complete description of the growth protocols can be found in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. 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).
|
| |
|
| 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 SMM medium until OD500 of 0.4_10 minutes after addition of 0.4 M NaCl_replicate 1
|
| 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 |
Feb 10, 2011 |
| Last update date |
Mar 07, 2012 |
| Contact name |
Ulrike Mäder |
| E-mail(s) |
[email protected]
|
| Organization name |
University Medicine Greifswald
|
| Department |
Functional Genomics
|
| Street address |
F.-L.-Jahn-Str. 15A
|
| City |
Greifswald |
| ZIP/Postal code |
D-17489 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13149 |
| Series (1) |
| GSE27219 |
The condition-dependent transcriptome of Bacillus subtilis 168 |
|
