Title: Evaluation of Tagseq, a Reliable Low-cost Alternative for Rnaseq 1

نویسندگان

  • Brian K. Lohman
  • Jesse N. Weber
  • Daniel I. Bolnick
چکیده

11 RNAseq is a relatively new tool for ecological genetics that offers researchers insight into changes 12 in gene expression in response to a myriad of natural or experimental conditions. However, standard 13 RNAseq methods (e.g., Illumina TruSeq or NEBNext) can be cost prohibitive, especially when 14 study designs require large sample sizes. Consequently, RNAseq is often underused as a method, or 15 is applied to small sample sizes that confer poor statistical power. Low cost RNAseq methods could 16 therefore enable far greater and more powerful applications of transcriptomics in ecological 17 genetics and beyond. Standard mRNAseq is costly partly because one sequences portions of the full 18 length of all transcripts. Such whole-mRNA data is redundant for estimates of relative gene 19 expression. TagSeq is an alternative method that focuses sequencing effort on mRNAs’ 3’ end, 20 thereby reducing the necessary sequencing depth per sample, and thus cost. Here we present a 21 revised TagSeq protocol, and compare its performance against NEBNext, the “gold-standard” 22 whole mRNAseq method. We built both TagSeq and NEBNext libraries from the same biological 23 samples, each spiked with control RNAs. We found that TagSeq measured the control RNA 24 distribution more accurately than NEBNext, for a fraction of the cost per sample (~10%). The 25 higher accuracy of TagSeq was particularly apparent for transcripts of moderate to low abundance. 26 Technical replicates of TagSeq libraries are highly correlated, and were correlated with NEBNext 27 results. Overall, we show that our modified TagSeq protocol is an efficient alternative to traditional 28 whole mRNAseq, offering researchers comparable data at greatly reduced cost. 29 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/036426 doi: bioRxiv preprint first posted online Jan. 11, 2016;

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Evaluation of TagSeq, a reliable low-cost alternative for RNAseq.

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تاریخ انتشار 2016