|
| Status |
Public on Oct 19, 2009 |
| Title |
arcZ_pJV300_BR2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Reference genomic DNA
|
| Organism |
Salmonella enterica |
| Characteristics |
reference: Salmonella enterica serovar Typhimurium SL1344 genomic DNA
|
| 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
|
| Label protocol |
Labelling protocol at http://www.ifr.ac.uk/Safety/Microarrays/default.html#protocols
|
| |
|
| Channel 2 |
| Source name |
arcZ_pJV300_BR2
|
| Organism |
Salmonella enterica |
| Characteristics |
cell (plasmid): Salmonella enterica serovar Typhimurium SL1344 delta arcZ (pJV300)
|
| Growth protocol |
ArcZ deletion mutant was grown in liquid culture inoculated 1:100 from an overnight culture for 6h after cells had reached an OD600=2.0 to reach late stationary phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation protocol 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
|
| |
|
| |
| 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, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| Description |
Intensity ratios of RNA (channel 2) divided by DNA (channel 1) 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.
|
| |
|
| Submission date |
Aug 23, 2009 |
| Last update date |
Oct 19, 2009 |
| Contact name |
Sacha Lucchini |
| E-mail(s) |
sacha.lucchini@bbsrc.ac.uk
|
| 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 |
GPL5780 |
| Series (1) |
| GSE17771 |
Specific and pleiotropic patterns of mRNA regulation by ArcZ |
|
