| Citation | Lamm AT, Stadler MR, Zhang H, Gent JI, Fire AZ. Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res, 2011. |
| PubMed ID | 21177965 |
| Short Description | Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. GEO Record: GSE22410 Platform: GPL9269 Download gene-centric, log2 transformed data: WBPaper00037948.ce.rs.csv |
| # of Conditions | 15 |
Full Description
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We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures. Experimental Details: RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP003783.SRX028190 RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP003783.SRX028191 RNASeq.elegans.WBStrain00022523.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP003783.SRX028192 RNASeq.elegans.WBStrain00000364.WBls:0000063.Hermaphrodite.WBbt:0007833.SRP003783.SRX028193 RNASeq.elegans.WBStrain00030567.WBls:0000002.Male.WBbt:0007833.SRP003783.SRX028194 RNASeq.elegans.WBStrain00030567.WBls:0000002.Male.WBbt:0007833.SRP003783.SRX028195 RNASeq.elegans.WBStrain00030566.WBls:0000038.Male.WBbt:0007833.SRP003783.SRX028196 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP003783.SRX028197 RNASeq.elegans.WBStrain00000001.WBls:0000027.Hermaphrodite.WBbt:0007833.SRP003783.SRX028198 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP003783.SRX028199 RNASeq.elegans.WBStrain00000001.WBls:0000038.Hermaphrodite.WBbt:0007833.SRP003783.SRX028200 RNASeq.elegans.WBStrain00000001.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP003783.SRX028201 RNASeq.elegans.WBStrain00000001.WBls:0000027.Hermaphrodite.WBbt:0007833.SRP003783.SRX028202 RNASeq.elegans.WBStrain00000001.WBls:0000035.Hermaphrodite.WBbt:0007833.SRP003783.SRX028203 RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP003783.SRX028204. |
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