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Sample GSM665084 Query DataSets for GSM665084
Status Public on May 28, 2011
Title PS-108-D0
Sample type RNA
 
Source name Persistent shedding pig at day 0 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): 0
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

Data table header descriptions
ID_REF
VALUE Log2, quantile-normalized signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 8.964162686
AFFX-BioB-5_at 7.553102007
AFFX-BioB-M_at 9.176902065
AFFX-BioC-3_at 7.87842905
AFFX-BioC-5_at 8.187113382
AFFX-BioDn-3_at 12.94845143
AFFX-BioDn-5_at 10.33129153
AFFX-CreX-3_at 13.77286716
AFFX-CreX-5_at 13.37985149
AFFX-DapX-3_at 11.26092542
AFFX-DapX-5_at 8.880849027
AFFX-DapX-M_at 11.0542365
AFFX-LysX-3_at 8.905916304
AFFX-LysX-5_at 6.014307883
AFFX-LysX-M_at 7.7190871
AFFX-PheX-3_at 8.968999015
AFFX-PheX-5_at 7.447220269
AFFX-PheX-M_at 7.59864971
AFFX-r2-Bs-dap-3_at 11.36392557
AFFX-r2-Bs-dap-5_at 10.26547292

Total number of rows: 24123

Table truncated, full table size 698 Kbytes.




Supplementary file Size Download File type/resource
GSM665084.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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