|
| Status |
Public on Oct 28, 2009 |
| Title |
WT_LEP_B1T1 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
WT_LEP_B1T1
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: Salmonella enterica serovar Typhimurium SL1344
growth stage: late-exponential
genotype/variation: wild type
|
| Growth protocol |
Strain was grown in LB inoculated 1:1000 from an overnight culture for 250min to reach the late-exponential phase of growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation protocol 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 |
Reference genomic DNA
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
strain: Salmonella enterica serovar Typhimurium SL1344
|
| Growth protocol |
S. Typhimurium grown to stationary phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)
|
| 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/default.html#protocols
|
| Scan protocol |
Axon GenePix4000A, 10um resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Description |
Intensity ratios of channel 1 (cDNA) divided by channel 2 (gDNA) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.
|
| 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. Flagged features are omitted from the data centring process. Because we used a microarray based on S. Typhimurium strain LT2 to analyse the transcriptional response of a different strain (S. Typhimurium strain SL1344), we removed all the data corresponding to genes present in LT2, but absent from SL1344.
|
| |
|
| Submission date |
Oct 06, 2009 |
| Last update date |
Oct 28, 2009 |
| Contact name |
Sacha Lucchini |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Food Research
|
| Department |
Molecular Microbiology
|
| Street address |
Colney Lane
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9091 |
| Series (2) |
| GSE18424 |
The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium |
| GSE18452 |
Role of stpA in Salmonella typhimurium |
|
