ArticleNucleic acids research2011
Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers.
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Who cites it
157 citing papers in PubMed.
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- A comparative analysis of Marburg virus-infected bat and human models from public high-throughput sequencing data.International journal of medical sciences · 2025Article
- An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families.bioRxiv : the preprint server for biology · 2024Article
- Quantitative design of cell type-specific mRNA stability from microRNA expression data.bioRxiv : the preprint server for biology · 2024Article
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- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
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97 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Deep sequencing of small RNAs (sRNA-seq) is now the gold standard for small RNA profiling and discovery. Biases in sRNA-seq have been reported, but their etiology remains unidentified. Through a comprehensive series of sRNA-seq experiments, we establish that the predominant cause of the bias is the RNA ligases. We further demonstrate that RNA ligases have strong sequence-specific biases which distort the small RNA profiles considerably. We have devised a pooled adapter strategy to overcome this bias, and validated the method through data derived from microarray and qPCR. In light of our findings, published small RNA profiles, as well as barcoding strategies using adapter-end modifications, may need to be revisited. Importantly, by providing a wide spectrum of substrate for the ligase, the pooled-adapter strategy developed here provides a means to overcome issues of bias, and generate more accurate small RNA profiles.
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