Author: Chang, Stewart T.; Sova, Pavel; Peng, Xinxia; Weiss, Jeffrey; Law, G. Lynn; Palermo, Robert E.; Katze, Michael G.
Title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line Document date: 2011_9_20
ID: zyzgk2z3_35
Snippet: Splice site variant detection and testing. The positions of known viral splice sites were found in the literature (44) , and the corresponding sequences were identified in strain pNL4-3 (GenBank accession no. AF003887). Based on sequence identity to strain LAI, a list of known LAI-specific splice sites was generated and compared to the NGS TopHat output. Splice patterns involving splice sites SD 1 and SA 2/2* were tested by quantitative PCR (qPCR.....
Document: Splice site variant detection and testing. The positions of known viral splice sites were found in the literature (44) , and the corresponding sequences were identified in strain pNL4-3 (GenBank accession no. AF003887). Based on sequence identity to strain LAI, a list of known LAI-specific splice sites was generated and compared to the NGS TopHat output. Splice patterns involving splice sites SD 1 and SA 2/2* were tested by quantitative PCR (qPCR) using primers PSK027F (5= CAGGGACTTG AAAGCGAAAG 3=; locations 193 to 212 in HIVBRUCG accession no. K02013) and PSK027R (5= TGGGGCTTGTTCCATCTATC 3=; locations 5136 to 5155).
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