|
| Status |
Public on Jul 03, 2013 |
| Title |
relA spoT ESP 3 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
SL1344 cDNA ∆relA ,∆spoT OD600 = 2.3 replicate 3
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
growth phase: early stationary
genotype/variation: ∆relA, ∆spoT
|
| Growth protocol |
Salmonella strains were innoculated 1/100 from 5 ml over night cultures into 25 ml Lb (10g NaCl) in 250 ml flasksand grown at 37°C in a shaking water bath. When the required OD600 was reached 10 ml culture was removed and mixed with 2 ml 5% Phenol, 95% Ethanol, shaken for 20 seconds then stored on ice for 20 min. Cells were then harvested by centrifugation and RNA extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| Label |
Cy5-dCTP
|
| Label protocol |
Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| |
|
| Channel 2 |
| Source name |
SL1344 genomic DNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
|
| Growth protocol |
Salmonella strains were innoculated 1/100 from 5 ml over night cultures into 25 ml Lb (10g NaCl) in 250 ml flasksand grown at 37°C in a shaking water bath. When the required OD600 was reached 10 ml culture was removed and mixed with 2 ml 5% Phenol, 95% Ethanol, shaken for 20 seconds then stored on ice for 20 min. Cells were then harvested by centrifugation and RNA extracted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| Label |
Cy3-dCTP
|
| Label protocol |
Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
|
| |
|
| |
| Hybridization protocol |
Slides blocked with DCE according to 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 and 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 usiong GenePix (Molecular Devices) .
|
| |
|
| Submission date |
Jul 02, 2013 |
| Last update date |
Jul 03, 2013 |
| 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 |
GPL5780 |
| Series (1) |
| GSE48478 |
Growth phase dependent gene expression of Salmonella Typhimurium SL1344 parental strain and isogenic ∆relA, ∆spoT ppGpp null strain |
|
