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Sample GSM299024 Query DataSets for GSM299024
Status Public on Jun 15, 2009
Title heifers with PI fetuses (BVDV), day 160 of pregnancy, 3rd replicate
Sample type RNA
 
Source name Total white blood cells from ncpBVDV-infected heifers with PI, TI or control fetuses
Organism Bos taurus
Characteristics Total white blood cells
Treatment protocol Blood sample collected at day160 of gestation
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed from Trireagent BD for blood derivatives according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 3.5 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).  
 
Hybridization protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse GeneChip 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GCOS Scanner 7G.
Description Gene expression after ncpBVDV infection
Data processing Data was analyzed with DChip 2006, build 12.21.06, using default settings for model-based summation of expression values, and following normalization to invariant set of probes. 
 
Submission date Jun 19, 2008
Last update date Jun 23, 2008
Contact name Kate McInnerney
E-mail(s) kmcinnerney@montana.edu
Phone 406-994-5666
Fax 406-994-4926
URL http://cores.montana.edu
Organization name Montana State University
Department Microbiology
Lab Functional Genomics Facility
Street address 109 Lewis Hall
City Bozeman
State/province MT
ZIP/Postal code 59717
Country USA
 
Platform ID GPL2112
Series (1)
GSE11835 Gene expression data in heifers with persistently infected (PI) or transiently infected (TI) fetuses.

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 183.78 P 0.000340305
AFFX-BioB-M_at 226.259 P 4.42873e-05
AFFX-BioB-3_at 134.805 P 7.00668e-05
AFFX-BioC-5_at 576.761 P 5.16732e-05
AFFX-BioC-3_at 705.105 P 4.42873e-05
AFFX-BioDn-5_at 1204.37 P 4.42873e-05
AFFX-BioDn-3_at 2135.14 P 7.00668e-05
AFFX-CreX-5_at 6115.58 P 4.42873e-05
AFFX-CreX-3_at 7269.13 P 4.42873e-05
AFFX-DapX-5_at 2.95395 A 0.382599
AFFX-DapX-M_at 4.43346 A 0.794268
AFFX-DapX-3_at 1.87891 A 0.772364
AFFX-LysX-5_at 7.85216 P 0.00933744
AFFX-LysX-M_at 2.1815 A 0.724871
AFFX-LysX-3_at 0.522922 A 0.659339
AFFX-PheX-5_at 0.421694 A 0.843268
AFFX-PheX-M_at 1.19519 A 0.814869
AFFX-PheX-3_at 6.03986 A 0.39692
AFFX-ThrX-5_at 0.662068 A 0.997133
AFFX-ThrX-M_at 1.58728 A 0.772364

Total number of rows: 24128

Table truncated, full table size 872 Kbytes.




Supplementary file Size Download File type/resource
GSM299024.CEL.gz 1.9 Mb (ftp)(http) CEL
GSM299024.CHP.gz 131.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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