ArticleSilence2012
Reducing ligation bias of small RNAs in libraries for next generation sequencing.
Article in Silence, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
124 citing papers in PubMed, 2 syntheses or guidelines pooled it, 199 citations in OpenAlex.
- Uncovering transcriptomic biomarkers for enhanced diagnosis of methamphetamine use disorder: a comprehensive review.Frontiers in psychiatry · 2023Pooled it
- A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species.Nucleic acids research · 2014Pooled it
- A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.Microbial genomics · 2026Article
- Review
- OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions.bioRxiv : the preprint server for biology · 2026Article
- Tissue specific RISC-loading reassesses small RNA functionality in developing pepper fruit.Plant molecular biology · 2026Article
- An absolute quantification atlas of small non-coding RNAs across diverse mammalian tissues and cell lines.Nature communications · 2026Article
- Identification of an enzyme with strong single-stranded DNA ligation activity and its application for sequencing.Nucleic acids research · 2025Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus.Nucleic acids research · 2024Article
- NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions.Nature communications · 2024Article
- Intrinsically disordered proteins SAID1/2 condensate on SERRATE for dual inhibition of miRNA biogenesis in Arabidopsis.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- YBX1-interacting small RNAs andJournal of bone oncology · 2023Article
- Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method.Science China. Life sciences · 2023Article
- choros: correction of sequence-based biases for accurate quantification of ribosome profiling data.bioRxiv : the preprint server for biology · 2023Article
- Preparation and processing of dried blood spots for microRNA sequencing.Biology methods & protocols · 2023Review
- The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes.Genes · 2022Article
- Exosome RNA Sequencing as a Tool in the Search for Cancer Biomarkers.Non-coding RNA · 2022Review
- Mechanistic insights into non-coding Y RNA processing.RNA biology · 2022Article
- Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.Nature biotechnology · 2021Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe use of nucleic acid-modifying enzymes has driven the rapid advancement in molecular biology. Understanding their function is important for modifying or improving their activity. However, functional analysis usually relies upon low-throughput experiments. Here we present a method for functional analysis of nucleic acid-modifying enzymes using next generation sequencing.
findingsWe demonstrate that sequencing data of libraries generated by RNA ligases can reveal novel secondary structure preferences of these enzymes, which are used in small RNA cloning and library preparation for NGS. Using this knowledge we demonstrate that the cloning bias in small RNA libraries is RNA ligase-dependent. We developed a high definition (HD) protocol that reduces the RNA ligase-dependent cloning bias. The HD protocol doubled read coverage, is quantitative and found previously unidentified microRNAs. In addition, we show that microRNAs in miRBase are those preferred by the adapters of the main sequencing platform.
conclusionsSequencing bias of small RNAs partially influenced which microRNAs have been studied in depth; therefore most previous small RNA profiling experiments should be re-evaluated. New microRNAs are likely to be found, which were selected against by existing adapters. Preference of currently used adapters towards known microRNAs suggests that the annotation of all existing small RNAs, including miRNAs, siRNAs and piRNAs, has been biased.
Identifiers
What OpenQuestion holds
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.