|
| Status |
Public on Dec 30, 2018 |
| Title |
WT_empty_3 |
| Sample type |
RNA |
| |
|
| Source name |
WT_empty
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
genotype: B. subtilis 168 amyE::spaRK pNZ8910
|
| Growth protocol |
The strains listed were grown in Luria Bertani broth O.D. 600nm 1.0, at which point subtilin was added to a final concentration of 1%. The cells were grown for a further two hours at which point the cells were harvested for RNA isolation.
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 |
Wild type parent strain with empty overexpression plasmid_rep3
|
| 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 17, 2012 |
| Last update date |
Dec 30, 2018 |
| 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) |
| GSE35916 |
Membrane protein overproduction stress in Bacillus subtilis |
|
