|
| Status |
Public on Aug 23, 2008 |
| Title |
HFQ_LB_SPI-1_BR2 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Reference genomic DNA
|
| Organism |
Salmonella enterica |
| Characteristics |
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 |
Channel Label Protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
| |
|
| Channel 2 |
| Source name |
HFQ_LB_SPI-1_BR2
|
| Organism |
Salmonella enterica |
| Characteristics |
Salmonella enterica serovar Typhimurium SL1344 hfq-
|
| Growth protocol |
S. Typhimurium grown under SPI-1 inducing conditions: overnight growth in LB-broth containing 0.3M NaCl, under oxygen tension.
|
| 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
|
| |
|
| |
| 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 1) divided by DNA (channel 2) 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 |
Sep 07, 2007 |
| Last update date |
Aug 14, 2011 |
| 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) |
| GSE8985 |
Effect of hfq-deletion on Salmonella transcriptome |
|
