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Sample GSM560393 Query DataSets for GSM560393
Status Public on Dec 01, 2010
Title Ferret Lung, uninfected, on Day 0, biological rep2
Sample type RNA
 
Source name Ferret
Organism Mustela putorius furo
Characteristics tissue: Lung
virus strain: Uninfected
Treatment protocol In experiments with SARS-CoV infection, intranasal infection of ferrets with 10^3 TCID SARS-CoV / Tor2 strain was performed. Ferrets were euthanized on day 0 (before infection), day 1 and day 2 (post infection). Peripheral blood was collected in PAXgene tubes ((BD®) and lung tissue was excised and put in RNAlater (Ambion, Austin, TX) immediately. In experiments with IFN-a2b, subcutaneous injection of ferrets with 1 microgram/kilogram of IFN-a2b was performed on the back of ferrets. Ferrets were euthanized on day 0 (before injection), day 1 and day 2 (post injection). Peripheral blood was collected in PAXgene tubes and lung tissue was excised and put in RNAlater (Ambion, Austin, TX) immediately.
Extracted molecule total RNA
Extraction protocol Total RNA from blood was extracted with PAXgene Blood RNA Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Total RNA from lung was extracted with TRIzol (Invitrogen) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Description Gene expression data from ferret lung, uninfected
Data processing The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.
 
Submission date Jun 25, 2010
Last update date Dec 01, 2010
Contact name Longsi Ran
E-mail(s) lran@uhnresearch.ca
Phone 416-581-7607
Organization name Toronto General Research Institute
Department Division of Experimental Therapeutics
Lab Dr. David J Kelvin
Street address 101 College Street
City Toronto
State/province ON
ZIP/Postal code M5G 1L7
Country Canada
 
Platform ID GPL3738
Series (1)
GSE22581 Early gene expression events in ferrets in response to SARS coronavirus infection versus direct interferon-alpha2b stimulation

Data table header descriptions
ID_REF
VALUE PLIER-calculated Signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 157.5381
AFFX-BioB-5_at 147.9445
AFFX-BioB-M_at 178.3667
AFFX-BioC-3_at 381.5896
AFFX-BioC-5_at 389.469
AFFX-BioDn-3_at 1208.02
AFFX-BioDn-5_at 862.4406
AFFX-Cfa-actin-3_s_at 1262.77
AFFX-Cfa-actin-5_at 925.7733
AFFX-Cfa-actin-5_s_at 3.544983
AFFX-Cfa-actin-M_x_at 415.9902
AFFX-Cfa-ef1a-3_x_at 2992.852
AFFX-Cfa-ef1a-5_at 6.477512
AFFX-Cfa-ef1a-M_x_at 232.3123
AFFX-Cfa-gapdh-3_x_at 1185.038
AFFX-Cfa-gapdh-5_x_at 13.39798
AFFX-Cfa-gapdh-M_x_at 10.62684
AFFX-Cfa-r2-Bs-dap-3_at 1460.703
AFFX-Cfa-r2-Bs-dap-5_at 29.73377
AFFX-Cfa-r2-Bs-dap-M_at 766.0318

Total number of rows: 43035

Table truncated, full table size 1233 Kbytes.




Supplementary file Size Download File type/resource
GSM560393.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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