|
| Status |
Public on Mar 07, 2012 |
| Title |
wild type_replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Bacillus subtilis 1012
|
| Organism |
Bacillus subtilis |
| Characteristics |
genotype/variation: wild type
strain: 1012
|
| Growth protocol |
B. subtilis wild-type and rho-mutant cells were grown aerobically at 37 °C in LB medium. Samples for tiling array analysis were taken at OD540 of 0.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the method described in (Eymann et al., 2002, J Bacteriol 184, 2500-2520) 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, 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 |
Bacillus subtilis_grown in LB medium_exponential phase
|
| Data processing |
The log2 expression signal 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)
The median of the signal across the chromosome was subtracted for normalization.
|
| |
|
| Submission date |
Feb 14, 2011 |
| Last update date |
Mar 07, 2012 |
| Contact name |
Ulrike Mäder |
| E-mail(s) |
ulrike.maeder@uni-greifswald.de
|
| 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 |
GPL13168 |
| Series (1) |
| GSE27303 |
Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho. |
|
