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Sample GSM261504 Query DataSets for GSM261504
Status Public on Sep 01, 2008
Title Porcine alveolar macrophages infected with PRRSV VR-2332 (12 hours)
Sample type SAGE
Anchor NlaIII
Tag Count 103140
Tag Length 10
 
Source name Porcine alveolar macrophages infected with PRRSV (12 hours)
Organism Sus scrofa
Characteristics Porcine alveolar macrophages (PAMs) from broncho-alveolar lavage of PRRSV- and PCV-free pigs (3 pigs). These cells were infected with PRRSV for 12 hours.
Treatment protocol T75 flasks (1 from each pig) were infected with PRRSV strain VR-2332 at an multiplicity of infection of 10 at 4C for 1 hour to synchronize the infection. The flasks were washed 2X, fresh medium added and incubated at 37C for 12 hours.
Growth protocol Cells from lavage from 3 pigs were resuspended in RPMI and placed in T75 flasks. Cells were allowed to adhere for 2 hours prior to mock infection. The flasks were placed at 4C for 1 hour then washed twice with medium. Cells from each pig were maintained separately.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from PAMs using the Qiagen RNeasy kit.
 
Description SAGE library was prepared by pooling equimolar amounts of RNA from the cells from the 3 pigs.
 
Submission date Jan 31, 2008
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 GPL1270
Series (1)
GSE10346 PRRSV-infection of porcine alveolar macrophages

Data table header descriptions
TAG
COUNT
TPM tags per million

Data table
TAG COUNT TPM
CGGCCGAAAT 9500 92107.81
TTTCGGGTTA 1786 17316.27
CGCTGGGTTC 1072 10393.64
GAATGTGCGC 836 8105.49
TTCCCACGGG 745 7223.19
TTCACTATGA 659 6389.37
GCCGAGTATC 645 6253.64
CATCTGCAGG 477 4624.78
GTTCTCGCCA 475 4605.39
AGGAGTTGAG 472 4576.30
ATGGGCTGGC 470 4556.91
ACCAGCCATT 457 4430.87
GTAAAAAAAA 416 4033.35
CAGCTGAATT 378 3664.92
ATTTTTTTTT 377 3655.23
GGCTTCGGCT 320 3102.58
GTGACCACGG 319 3092.88
GCAGTCAGCC 307 2976.54
TAGGTTGTCT 301 2918.36
CTGAGAAACT 287 2782.63

Total number of rows: 32682

Table truncated, full table size 585 Kbytes.




Supplementary data files not provided

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