|
| Status |
Public on Jan 01, 2013 |
| Title |
Tennessee control-1 |
| Sample type |
RNA |
| |
|
| Source name |
S. Tennessee 20h culture
|
| Organism |
Salmonella enterica subsp. enterica serovar Tennessee |
| Characteristics |
strain: Tennessee
treatment: control
|
| Treatment protocol |
For each strain approximately 8 log CFU in 0.1M PBS were added onto a sterile filter paper disc and stored in a desiccator at 11% equillibrated relative humidity for 2 h.
|
| Growth protocol |
Salmonella Tennessee strain K4643 (Tennessee) and Typhimurium LT2 ATCC strain 19585 (LT2) were grown in Tryptic Soy Broth at 37ºC with orbital shaking for 20h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated (Rneasy Mini Kit, Qiagen Inc., CA) and confirmed for quality (Agilent 2100 Bioanalyzer, Agilent Technologies, Inc., Santa Clara, CA) following the manufacturers’ instructions.
|
| Label |
Alexa-555
|
| Label protocol |
First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer. cRNA was fragmented to uniform size and verified on the Bioanalyzer.
|
| |
|
| Hybridization protocol |
1 µg of purified cRNA was fragmented to uniform size and applied to a custom Agilent 4x44K microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.
|
| Scan protocol |
Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.
|
| Description |
stationary culture, 2h desiccation
|
| Data processing |
Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).
|
| |
|
| Submission date |
Aug 15, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Haiping Li |
| Organization name |
Food and Drug Administration
|
| Department |
CFSAN/OFS/Moffett Center
|
| Street address |
6502 S. Archer Rd
|
| City |
Bedford Park |
| State/province |
IL |
| ZIP/Postal code |
60501 |
| Country |
USA |
| |
|
| Platform ID |
GPL15942 |
| Series (1) |
| GSE40146 |
Comparative Transcriptomic Analysis of Salmonella in Desiccation |
|
