ArticleRNA (New York, N.Y.)2020
Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 11 citations in OpenAlex.
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- Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.Journal of molecular evolution · 2023Review
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- Dynamic RNA Fitness Landscapes of a Group I Ribozyme during Changes to the Experimental Environment.Molecular biology and evolution · 2022Article
- Experimental Resurrection of Ancestral Mammalian CPEB3 Ribozymes Reveals Deep Functional Conservation.Molecular biology and evolution · 2021Article
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Authors and funding
4 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
In vitro selection combined with high-throughput sequencing is a powerful experimental approach with broad application in the engineering and characterization of RNA molecules. Diverse pools of starting sequences used for selection are often flanked by fixed sequences used as primer binding sites. These low diversity regions often lead to data loss from complications with Illumina image processing algorithms. A common method to alleviate this problem is the addition of fragmented bacteriophage PhiX genome, which improves sequence quality but sacrifices a portion of usable sequencing reads. An alternative approach is to insert nucleotides of variable length and composition ("phased inserts") at the beginning of each molecule when adding sequencing adaptors. This approach preserves read depth but reduces the length of each read. Here, we test the ability of phased inserts to replace PhiX in a low-diversity sample generated for a high-throughput sequencing based ribozyme activity screen. We designed a pool of 4096 RNA sequence variants of the self-cleaving twister ribozyme from
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