ArticleNucleic acids research2019
SMARTer single cell total RNA sequencing.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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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.
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Who cites it
33 citing papers in PubMed, 61 citations in OpenAlex.
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Uli-epic: profiling RNA modifications from ultra-low input samples.Genome biology · 2025Article
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 2024Article
- Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.Clinical and translational medicine · 2024Article
- Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3.Cell discovery · 2024Article
- Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.Frontiers in genetics · 2024Article
- A new and effective two-step clustering approach for single cell RNA sequencing data.BMC genomics · 2023Article
- Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells.Cancer research · 2023Article
- Decoding the lncRNAome Across Diverse Cellular Stresses Reveals Core p53-effector Pan-cancer Suppressive lncRNAs.Cancer research communications · 2023Article
- Best practice standards for circular RNA research.Nature methods · 2022Review
- Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing.Nature communications · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches.Frontiers in genetics · 2022Review
- Comprehensive elaboration of circular RNA in multiple myeloma.Frontiers in pharmacology · 2022Review
- Research progress on circular RNA vaccines.Frontiers in immunology · 2022Review
- Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Advances in Non-Coding RNA Sequencing.Non-coding RNA · 2021Review
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3' end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.
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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.