|
| Status |
Public on Jun 22, 2015 |
| Title |
168_Dhfq_1 |
| Sample type |
RNA |
| |
|
| Source name |
Bacillus subtilis cells
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
genotype/variation: hfq deletion mutant
growth phase: exponential phase
|
| Growth protocol |
B. subtilis strains (wild-type and mutants) were grown in LB medium 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 using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).
|
| |
|
| Hybridization protocol |
Hybridization was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).
|
| Scan protocol |
Scanning was performed by PartnerChip (Evry, France) as described in Nicolas et al (2012) (PMID:22383849).
|
| Description |
hfq mutant replicate 1
168_ymaH_1.530779A03
|
| 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). Data were quantile normalized using LIMMA package.
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 |
Mar 13, 2015 |
| Last update date |
Jun 22, 2015 |
| Contact name |
Tatiana Rochat |
| E-mail(s) |
tatiana.rochat@jouy.inra.fr
|
| Organization name |
INRA
|
| Lab |
Virologie et Immunologie Moléculaires
|
| Street address |
Domaine de Vilvert
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL19890 |
| Series (2) |
| GSE66891 |
Tracking the elusive function of Bacillus subtilis Hfq (NimbleGen) |
| GSE66893 |
Tracking the elusive function of Bacillus subtilis Hfq |
|
