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Sample GSM154617 Query DataSets for GSM154617
Status Public on Jun 30, 2007
Title Bovine BL3 cells acutely infected with BVDV2 strain 296c
Sample type SAGE
Anchor NlaIII
Tag Count 91868
Tag Length 10
 
Source name Bovine BL3 cells infected with BVDV2 strain 296c
Organism Bos taurus
Characteristics Bovine BL3 cells - B cell lymphosarcoma cell line, nonadherent. BL3 cells had acute infection with BVDV2 strain 296c. The cells were collected at 18 hours post-infection before signs of cytopathic effect were visible. Immunohistochemistry examination of culture showed >90% of the cells were infected.
Treatment protocol BL3 cells were infected with BVDV strain 296c at MOI of 2. Cells were collected at 18 hours post-infection.
Growth protocol BL3 cells were grown in Leibovitz MEM with Earles salts medium supplemented with 1.4 mM glutamate.
Extracted molecule total RNA
Extraction protocol Cells were collected by centrifugation and washed once with PBS. The cell pellet was resuspended and the cells lysed by addition of Trizol Reagent. The total RNA was prepared according to manufacturer's specifications.
 
Description SAGE library construction was done using the microSAGE protocol.
Data processing Tag sequences were extracted using SAGE 2000 ver. 4.0 software.
 
Submission date Jan 10, 2007
Last update date Nov 19, 2008
Contact name John D. Neill
E-mail(s) john.neill@ars.usda.gov
Phone 515-663-7730
Organization name National Animal Disease Center
Lab VPDLRU
Street address 2300 Dayton Ave.
City Ames
State/province IA
ZIP/Postal code 50010
Country USA
 
Platform ID GPL223
Series (1)
GSE6704 Gene expression changes in BVDV2-infected BL3 cells

Data table header descriptions
TAG Tag sequence
COUNT Number of times tag sequence appears
TPM tags per million

Data table
TAG COUNT TPM
GCCGGCCCGG 1393 15163.06
GGCTTCGGCT 1337 14553.49
GCCTGATGGG 1169 12724.78
CTGCCCAGCG 1151 12528.85
GGCTTTGGTC 1083 11788.65
GCCGAGGAAG 968 10536.86
CCCCAGCCGG 881 9589.85
TCGGTCTGGG 734 7989.72
CTGGGAAATT 691 7521.66
AAGCCCAGCG 661 7195.11
GACGACACGA 613 6672.62
GGCAAGCCCC 573 6237.21
GCTGCCATCC 557 6063.05
GTTCGTGCCA 517 5627.64
GGTCACCAGC 514 5594.98
GGAGGCGCTA 513 5584.10
TCCGTGCACC 512 5573.21
CCCAGCCACT 507 5518.79
GCAGAGTTCG 497 5409.94
AGGAAAGCGG 470 5116.04

Total number of rows: 21314

Table truncated, full table size 398 Kbytes.




Supplementary data files not provided

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