B. subtilis strains (wild-type and mutants) were grown in LB medium at 37°C and harvested by centrifigution during the exponential phase of growth.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted as described in Nicolas et al (2012) (PMID:22383849)
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). 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). 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) or by PartnerChip (Evry, France) following their standard operating protocol.
Scan protocol
Scanning was performed by Roche NimbleGen (Madison, WI USA) or by PartnerChip (Evry, France) following their standard operating protocol.
Description
strain CB169 replicate1
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 as described in (Nicolas et al., 2012 PMID: 22383849). 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).
