Selected article for: "duplex length and siRNA read count"
Author: Chang Liu; Ze Chen; Wenyuan Shen; Deshui Yu; Siyu Li; Yue Hu; Haishuo Ji; Wenjun Bu; Qingsong Wang; Shan Gao
Title: Complemented palindrome small RNAs first discovered from SARS coronavirus
  • Document date: 2017_9_7
    • ID: g55d5ijx_9
    Snippet: In this study, 11 invertebrate viruses were detected using 51 runs of sRNA-seq data (Supplementary 100 file 1) and two mammal viruses (H1N1 and SARS-CoV) were detected using 12 runs of sRNA-seq data. In 101 our previous study, six mammal viruses were detected using 36 runs of sRNA-seq data [6] . The detection of 102 siRNA-duplexes by 11 invertebrate and eight mammal viruses was performed using a published program in 103 our previous study [7] . T.....
    Document: In this study, 11 invertebrate viruses were detected using 51 runs of sRNA-seq data (Supplementary 100 file 1) and two mammal viruses (H1N1 and SARS-CoV) were detected using 12 runs of sRNA-seq data. In 101 our previous study, six mammal viruses were detected using 36 runs of sRNA-seq data [6] . The detection of 102 siRNA-duplexes by 11 invertebrate and eight mammal viruses was performed using a published program in 103 our previous study [7] . Then, we compared the features of siRNA duplexes induced by invertebrate viruses 104 ( Figure 1A ) with those induced by plant viruses ( Figure 1B) . The results showed that the duplex length was 105 the principal factor to determine the read count in both plants and invertebrates. 21-nt siRNA duplexes were 106 the most abundant duplexes in both plants and invertebrates, followed by 22-nt siRNA duplexes in plants 107 but 20-nt siRNA duplexes in invertebrates. 21-nt siRNA duplexes with 2-nt overhangs were the most 108 abundant 21-nt duplexes in plants, while 21-nt siRNA duplexes with 1-nt overhangs were the most abundant 109 21-nt duplexes in invertebrates but they had a very close read count to that of 21-nt siRNA duplexes with 2-110 nt overhangs. 18-nt, 19-nt, 20-nt and 22-nt siRNA duplexes in invertebrates had much higher percentages of 111 total sequenced reads that those in plants. In addition, 18-nt and 19-nt siRNA duplexes had very close read 112 counts and 20-nt and 22-nt siRNA duplexes had very close read counts in invertebrates. Since siRNA 113 duplexes induced by mammal viruses had significantly lower percentages of total sequenced reads, the 114 comparison of siRNA-duplex features between mammals and invertebrates/or plants could not provide 115 meaningful results using the existing public data with standard sequencing depth. However, as an 116 unexpected result from siRNA-duplex analysis, we discovered cpsRNAs from invertebrate and mammal 117 viruses. 118

    Search related documents: