ArticleRNA (New York, N.Y.)2018
Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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
18 citing papers in PubMed.
- MitoClipSplice: a machine learning framework for resolving mitochondrial RNA cleavage sites from strand-specific RNA-seq soft-clips.Briefings in bioinformatics · 2026Article
- Transcriptomic Profiling Identifies Key Genes and ERBB Signaling Pathway Associated with Aggressive Behavior in Muscovy Ducks (Animals : an open access journal from MDPI · 2026Article
- Strand-specific detection of cell-associated sense and antisense HIV-1 RNAs in splenocytes and PBMC from PLWH.Retrovirology · 2025Article
- Artifacts and biases of the reverse transcription reaction in RNA sequencing.RNA (New York, N.Y.) · 2023Review
- TargetedCell reports methods · 2023Article
- A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers.Nature biotechnology · 2022Article
- Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries.BMC genomics · 2022Article
- Article
- Article
- Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival.Cancer research · 2021Article
- Review
- Conserved DNA sequence features underlie pervasive RNA polymerase pausing.Nucleic acids research · 2021Article
- Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly.Angewandte Chemie (International ed. in English) · 2020Article
- Nascent RNA analyses: tracking transcription and its regulation.Nature reviews. Genetics · 2019Review
- Article
- Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction.Scientific reports · 2019Article
- MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network.Genome research · 2019Article
- PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma.PloS one · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Nonspecific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published data sets. We show that mispriming can occur with as little as two bases of complementarity at the 3' end of the primer followed by intermittent regions of complementarity. We also provide a computational pipeline that identifies cDNA reads produced from RT mispriming, allowing users to filter them out from any aligned data set. Using this analysis pipeline, we identify thousands of mispriming events in a dozen published data sets from diverse technologies including short RNA-seq, total/mRNA-seq, HITS-CLIP, and GRO-seq. We further show how RT mispriming can lead to misinterpretation of data. In addition to providing a solution to computationally remove RT-misprimed reads, we also propose an experimental solution to completely avoid RT-mispriming by performing RNA-seq using thermostable group II intron derived reverse transcriptase (TGIRT-seq).
Indexed as
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.