|
| Status |
Public on May 31, 2015 |
| Title |
ppGpp_dksA_R2_OD42 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
S. Typhimurium ΔrelAΔspoTΔdksA. Biol. Rep. 2_optical density (600 nm) of 4.2
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
|
| Treatment protocol |
Where appropriate 1µm cortisol added.
|
| Growth protocol |
Grown aerobically at 370C with shaking at 250rpm in minimal medium MM5.8 (Erikkson et al., 2006 Inf & Imm., 74:1243) to stationary phase overnight
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Label |
Cy5
|
| Label protocol |
Labelling according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| |
|
| Channel 2 |
| Source name |
S. Typhimurium SL1344 genomic DNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: SL1344
|
| Treatment protocol |
Where appropriate 1µm cortisol added.
|
| Growth protocol |
Grown aerobically at 370C with shaking at 250rpm in minimal medium MM5.8 (Erikkson et al., 2006 Inf & Imm., 74:1243) to stationary phase overnight
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA extracted according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Label |
Cy3
|
| Label protocol |
Labelling according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| |
|
| |
| Hybridization protocol |
Hybridisation according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Scan protocol |
GenePix 4000A at 10µm resolution
|
| Description |
Biol. Rep. 2 of 3
|
| Data processing |
Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated usiong BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using the block median
|
| |
|
| Submission date |
Nov 28, 2014 |
| Last update date |
May 31, 2015 |
| Contact name |
Arthur Thompson |
| E-mail(s) |
arthur.thompson@ifr.ac.uk
|
| Phone |
01603 255181
|
| Organization name |
Institute of Food Research
|
| Street address |
Colney Lane
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13609 |
| Series (2) |
| GSE63713 |
Transcriptomic profiles of S. Typhimurium SL1344 parent strain and ΔdksA and ΔrelAΔspoTΔdksA mutant strains grown to various optical densities during late-log and stationary phase in LB aerobic batch culture |
| GSE63715 |
Transcriptional profiles of Salmonella Typhimurium 4/74 parent and relA spoT, rpoS and dksA strains during stationary phase, and RNA polymerase distribution as determined by chromatin immunoprecipitation in parent, relA spoT and dksA strains |
|
