ArticleGenome research2011
Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms.Nucleic acids research · 2020Article
- Selection and gene flow shape niche-associated variation in pheromone response.Nature ecology & evolution · 2019Article
- Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma.The EMBO journal · 2019Article
- Decreasing miRNA sequencing bias using a single adapter and circularization approach.Genome biology · 2018Article
- QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs.Genome biology · 2018Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria.Bio-protocol · 2018Article
- Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project.Journal of visualized experiments : JoVE · 2017Article
- All the microbiology nematodes can teach us.FEMS microbiology ecology · 2016Article
- High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.RNA (New York, N.Y.) · 2016Article
- Transcriptome-wide investigation of circular RNAs in rice.RNA (New York, N.Y.) · 2015Article
- Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.Nature protocols · 2015Article
- Differential regulation of germline apoptosis in response to meiotic checkpoint activation.Genetics · 2014Article
- Article
- Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.BMC genomics · 2014Article
- The influences of PRG-1 on the expression of small RNAs and mRNAs.BMC genomics · 2014Article
- Article
- Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing.RNA (New York, N.Y.) · 2013Article
- Article
- Long noncoding RNAs in C. elegans.Genome research · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.