|
| Status |
Public on Jan 02, 2013 |
| Title |
rasP mutant_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
rasP mutant
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
genotype/variation: rasP mutant
|
| Growth protocol |
B. subtilis 168 and respective mutants were grown in Luria Bertani broth O.D. 600nm 1.0
The complete description of the growth protocols can be found in Zweers 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 LB medium_O.D. 600nm 1.0
rasP_2
|
| 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 |
Jan 20, 2012 |
| Last update date |
Jan 02, 2013 |
| Contact name |
Emma L Denham |
| E-mail(s) |
e.l.denham@warwick.ac.uk
|
| Organization name |
University of Warwick
|
| Department |
Warwick Medical School
|
| Lab |
Division of Microbiology and Infection
|
| Street address |
Gibbet Hill Road
|
| City |
Coventry |
| ZIP/Postal code |
CV4 |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15150 |
| Series (1) |
| GSE35236 |
Definition of the σ(W) Regulon of Bacillus subtilis in the Absence of Stress |
|
