ArticleNucleic acids research2015
Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 41 citations in OpenAlex.
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- Harnessing genomics for fast development and commercial introduction of high-resistant tomato varieties to Tomato Brown Rugose Fruit Virus.Breeding science · 2026Article
- Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling.Nature communications · 2025Article
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- Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection ofViruses · 2021Article
- WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data.F1000Research · 2021Article
- Molecular and Functional Characterization of the Somatic PIWIL1/piRNA Pathway in Colorectal Cancer Cells.Cells · 2019Article
- Bias-minimized quantification of microRNA reveals widespread alternative processing and 3' end modification.Nucleic acids research · 2019Article
- Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.Methods (San Diego, Calif.) · 2019Review
- miRge 2.0 for comprehensive analysis of microRNA sequencing data.BMC bioinformatics · 2018Article
- Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation duringeLife · 2018Article
- Reference standards for next-generation sequencing.Nature reviews. Genetics · 2017Review
- Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data.Scientific reports · 2017Article
- Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host-pathogen transcriptomes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Formidable challenges to the notion of biologically important roles for dietary small RNAs in ingesting mammals.Genes & nutrition · 2017Review
- Cajal body function in genome organization and transcriptome diversity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Toward the promise of microRNAs - Enhancing reproducibility and rigor in microRNA research.RNA biology · 2016Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is an increasing interest in complementing RNA-seq experiments with small-RNA (sRNA) expression data to obtain a comprehensive view of a transcriptome. Currently, two main experimental challenges concerning sRNA-seq exist: how to check the size distribution of isolated sRNAs, given the sensitive size-selection steps in the protocol; and how to normalize data between samples, given the low complexity of sRNA types. We here present two separate sets of synthetic RNA spike-ins for monitoring size-selection and for performing data normalization in sRNA-seq. The size-range quality control (SRQC) spike-in set, consisting of 11 oligoribonucleotides (10-70 nucleotides), was tested by intentionally altering the size-selection protocol and verified via several comparative experiments. We demonstrate that the SRQC set is useful to reproducibly track down biases in the size-selection in sRNA-seq. The external reference for data-normalization (ERDN) spike-in set, consisting of 19 oligoribonucleotides, was developed for sample-to-sample normalization in differential-expression analysis of sRNA-seq data. Testing and applying the ERDN set showed that it can reproducibly detect differential expression over a dynamic range of 2(18). Hence, biological variation in sRNA composition and content between samples is preserved while technical variation is effectively minimized. Together, both spike-in sets can significantly improve the technical reproducibility of sRNA-seq.
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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.