|
| Status |
Public on May 28, 2011 |
| Title |
PS-108-D2 |
| Sample type |
RNA |
| |
|
| Source name |
Persistent shedding pig at day 2 of post inoculation
|
| Organism |
Sus scrofa |
| Characteristics |
animal#: 108
shedding type: persistent shedding (PS) pig
infection: Salmonella enterica serovar Typhimurium (ST)
time (days post-infection): 2
tissue: peripheral blood
|
| Treatment protocol |
The pigs were intranasal challenge with 109 colony forming units (cfu) of nalidixic acid resistant ST c4232 at 7 weeks of age. Fecal and blood samples were collected from each animal at 0, 2, 7, 14, and 20 dpi.
|
| Growth protocol |
The piglets were raised in climate-controlled, fully enclosed isolation facilities at the USDA-ARS-National Animal Disease Center (NADC) in Ames, IA. The pigs tested fecal negative for Salmonella three times before challenge with Salmonella.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from 4.5-9.0 ml of solution from the PAXgene Blood RNA tubes using the PAXgene Blood RNA kit (Qiagen, Cat. no. 762164). The DNA was removed by in-solution DNase I digestion and RNeasy mini elute kit cleanup as recommended by QIAGEN.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared by the GeneChip® One-Cycle target labeling kit according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 6.5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Porcine Genome Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (affymetrix).
|
| Data processing |
The data were extracted by Affy (R package) using default settings and global scaling by quantile normalization method.
|
| |
|
| Submission date |
Feb 01, 2011 |
| Last update date |
May 28, 2011 |
| Contact name |
Chris Tuggle |
| E-mail(s) |
[email protected]
|
| Organization name |
Iowa State University
|
| Street address |
Kildee Hall 2255
|
| City |
Ames |
| ZIP/Postal code |
50010 |
| Country |
USA |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE27000 |
Peripheral blood transcriptome responses to Salmonella Typhimurium in pigs differing in Salmonella shedding phenotypes |
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