ArticleScientific reports2018
Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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Who cites it
21 citing papers in PubMed, 45 citations in OpenAlex.
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- Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes.Mobile DNA · 2024Article
- Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development.Nature communications · 2023Article
- Data Mining of Microarray Datasets in Translational Neuroscience.Brain sciences · 2023Review
- Single-Cell Multiomics.Annual review of biomedical data science · 2023Review
- Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.Bioinformatics (Oxford, England) · 2023Article
- Current challenges and best practices for cell-free long RNA biomarker discovery.Biomarker research · 2022Review
- A comparative analysis of single cell small RNA sequencing data reveals heterogeneous isomiR expression and regulation.Scientific reports · 2022Article
- ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data.BMC bioinformatics · 2022Article
- Accurate Prediction of Protein Sequences for Proteogenomics Data Integration.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Preparation of long single-strand DNA concatemers for high-level fluorescence in situ hybridization.Communications biology · 2021Article
- Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering.Life (Basel, Switzerland) · 2021Article
- Temporal single-cell regeneration studies: the greatest thing since sliced pancreas?Trends in endocrinology and metabolism: TEM · 2021Review
- Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing.Biology · 2021Review
- Single-cell RNA sequencing in human lung cancer: Applications, challenges, and pathway towards personalized therapy.Journal of the Chinese Medical Association : JCMA · 2021Review
- Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis.Frontiers in neuroscience · 2021Review
- DNA synthesis for true random number generation.Nature communications · 2020Article
- Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery.Genome biology · 2020Article
- RNA sequencing: the teenage years.Nature reviews. Genetics · 2019Review
- Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Attaching Unique Molecular Identifiers (UMI) to RNA molecules in the first step of sequencing library preparation establishes a distinct identity for each input molecule. This makes it possible to eliminate the effects of PCR amplification bias, which is particularly important where many PCR cycles are required, for example, in single cell studies. After PCR, molecules sharing a UMI are assumed to be derived from the same input molecule. In our single cell RNA-Seq studies of Physcomitrella patens, we discovered that reads sharing a UMI, and therefore presumed to be derived from the same mRNA molecule, frequently map to different, but closely spaced locations. This behaviour occurs in all such libraries that we have produced, and in multiple other UMI-containing RNA-Seq data sets in the public domain. This apparent paradox, that reads of identical origin map to distinct genomic coordinates may be partially explained by PCR stutter, which is often seen in low-entropy templates and those containing simple tandem repeats. In the absence of UMI this artefact is undetectable. We show that the common assumption that sequence reads having different mapping coordinates are derived from different starting molecules does not hold. Unless taken into account, this artefact is likely to result in over-estimation of certain transcript abundances, depending on the counting method employed.
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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.