|
| Status |
Public on Jan 25, 2016 |
| Title |
pBAD-ctr.2 (control) |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Salmonella enterica SL1344_pBAD-ctr_genomic DNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
genotype/variation: carrying pBAD-ctr
treated with: 0.2% (final conc.) L-arabinose
time point: 10 min post treatment
|
| Treatment protocol |
At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.
|
| Growth protocol |
Salmonella carrying pBAD-ctr or pBAD-SdsR were grown in LB-media to OD=1.5.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit
|
| Label |
Cy5
|
| Label protocol |
total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System
|
| |
|
| Channel 2 |
| Source name |
Salmonella enterica SL1344_pBAD-ctr_total RNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
genotype/variation: carrying pBAD-SdsR
treated with: 0.2% (final conc.) L-arabinose
time point: 10 min post treatment
|
| Treatment protocol |
At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.
|
| Growth protocol |
Salmonella carrying pBAD-ctr or pBAD-SdsR were grown in LB-media to OD=1.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit
|
| Label |
Cy3
|
| Label protocol |
total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System
|
| |
|
| |
| Hybridization protocol |
Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Scan protocol |
Axon GenePix4000A, 10nm resolution scan
|
| Data processing |
Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. pBAD-ctr serves as control for pBAD-SdsR.
|
| |
|
| Submission date |
Jan 24, 2016 |
| Last update date |
Jan 25, 2016 |
| Contact name |
Kai Papenfort |
| Organization name |
IMIB Würzburg
|
| Department |
RNA Biology
|
| Street address |
Josef-Schneider Str.2/BAU D15
|
| City |
Würzburg |
| State/province |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5780 |
| Series (1) |
| GSE77157 |
The target spectrum of SdsR small RNA in Salmonella |
|
