|
| Status |
Public on Jul 26, 2011 |
| Title |
∆scsA stationary phase, rep2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
S. Typhimurium, ∆scsA, stationary phase
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: 112910a
growth phase: stationary
genotype: ∆scsA
|
| Treatment protocol |
None.
|
| Growth protocol |
Stationary phase cultures were obtained by aerated, overnight culture at 37 °C in 5 mL LB in 50 mL flasks. To obtain highly invasive late logarithmic cultures, 2 µL of a stationary phase culture was inoculated in 5 mL LB and grown for 5 hours at 37 °C without aeration.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| Label |
Cy5
|
| Label protocol |
Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| |
|
| Channel 2 |
| Source name |
S. typhimurium genomic DNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: 112910a
sample type: reference
|
| Treatment protocol |
None.
|
| Growth protocol |
Stationary phase cultures were obtained by aerated, overnight culture at 37 °C in 5 mL LB in 50 mL flasks. To obtain highly invasive late logarithmic cultures, 2 µL of a stationary phase culture was inoculated in 5 mL LB and grown for 5 hours at 37 °C without aeration.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| Label |
Cy3
|
| Label protocol |
Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| |
|
| |
| Hybridization protocol |
Slides were blocked with DCE according to the protocol at PMID 11266573. For hybridisation and washing protocols, see http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| Scan protocol |
Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Data processing |
Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using block median normalization.
|
| |
|
| Submission date |
Jul 25, 2011 |
| Last update date |
Jul 26, 2011 |
| Contact name |
Neil Shearer |
| E-mail(s) |
neil.shearer@ifr.ac.uk
|
| Organization name |
Institute of Food Research
|
| Department |
Gut Health and Food Safety
|
| Lab |
Salmonella
|
| Street address |
Colney Lane
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR47UA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13609 |
| Series (1) |
| GSE30924 |
Salmonella Typhimurium: wild type vs. ∆scsA mutant |
|
