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Sample GSM176536 Query DataSets for GSM176536
Status Public on Jun 01, 2007
Title MLN_ST non_infected pig, rep1
Sample type RNA
 
Source name mesenteric lymph nodes, non-infected pig
Organism Sus scrofa
Characteristics Age: 7 weeks old pigs were used for this experiment
Treatment protocol Fifteen piglets from Salmonella spp.-free sows were weaned at 10 days (d) of age, shipped to the National Animal Disease Center, Ames, IA, and raised in isolation facilities. To confirm that all piglets were free of Salmonella spp. prior to challenge, bacteriological cultures were performed twice on rectal swabs before the experiments. At seven weeks of age, 3 pigs were randomly allocated to the non-infected group and 12 to the infected group. The three non-infected control pigs were necropsied 2 days prior to experimental infection. On day0, pigs in the infected groups were intranasally challenged with 1 x 109 CFU of S. Typhimurium ?4232. A randomly chosen group of three infected pigs were necropsied at each time point of 8 hpi, 24 hpi, 48 hpi and 21 dpi, respectively
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from ~200 mg of porcine MLN tissues by using the RNeasy Midi kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) based on the manufacture’s protocol
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).
Description Gene expression data from the mesenteric lymph nodes of non-infected pig
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
 
Submission date Mar 19, 2007
Last update date Jun 01, 2007
Contact name Christopher K Tuggle
E-mail(s) cktuggle@iastate.edu
Phone 515-294-4252
Fax 515-294-2401
URL http://www.public.iastate.edu/~ans/faculty/tuggle.html
Organization name Iowa State University
Department Animal Science
Lab Molecular Genetics
Street address 2255 Kildee Hall
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platform ID GPL3533
Series (1)
GSE7313 Expression data from non-infected and Salmonella Typhimurium infected mesenteric lymph nodes

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 457.842 P 0.000445901
AFFX-BioB-M_at 488.389 P 4.42873e-05
AFFX-BioB-3_at 357.105 P 4.42873e-05
AFFX-BioC-5_at 1101.27 P 5.16732e-05
AFFX-BioC-3_at 1414.37 P 5.16732e-05
AFFX-BioDn-5_at 2283.71 P 4.42873e-05
AFFX-BioDn-3_at 4280.94 P 5.16732e-05
AFFX-CreX-5_at 12323.4 P 5.16732e-05
AFFX-CreX-3_at 15569.3 P 4.42873e-05
AFFX-DapX-5_at 967.68 P 4.42873e-05
AFFX-DapX-M_at 1733.3 P 7.00668e-05
AFFX-DapX-3_at 2500.87 P 4.42873e-05
AFFX-LysX-5_at 145.853 P 6.02111e-05
AFFX-LysX-M_at 157.294 P 0.00359458
AFFX-LysX-3_at 350.371 P 5.16732e-05
AFFX-PheX-5_at 199.58 P 4.42873e-05
AFFX-PheX-M_at 312.166 P 4.42873e-05
AFFX-PheX-3_at 279.558 P 0.000581214
AFFX-ThrX-5_at 264.003 P 5.16732e-05
AFFX-ThrX-M_at 428.297 P 4.42873e-05

Total number of rows: 24123

Table truncated, full table size 901 Kbytes.




Supplementary file Size Download File type/resource
GSM176536.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM176536.EXP.gz 490 b (ftp)(http) EXP
Raw data provided as supplementary file

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