ArticleNature biotechnology2023
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 51 citations in OpenAlex.
- Hi-C for genome-wide detection of enhancer-hijacking rearrangements in routine lymphoid cancer biopsies.Cell genomics · 2026Article
- Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid.Microbiology spectrum · 2026Article
- Constellation illuminates rare disease genetics.medRxiv : the preprint server for health sciences · 2025Article
- The utility of ultra-deep RNA sequencing in Mendelian disorder diagnostics.American journal of human genetics · 2025Article
- Article
- An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin.bioRxiv : the preprint server for biology · 2025Article
- Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.Nature methods · 2025Article
- Transcriptome-wide analysis of differential expression in perturbation atlases.Nature genetics · 2025Article
- An overview of computational methods in single-cell transcriptomic cell type annotation.Briefings in bioinformatics · 2025Review
- A genome-wide atlas of human cell morphology.Nature methods · 2025Article
- Bidirectional epigenetic editing reveals hierarchies in gene regulation.Nature biotechnology · 2025Article
- Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.Nature cell biology · 2025Article
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing.NAR genomics and bioinformatics · 2024Article
- Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing.bioRxiv : the preprint server for biology · 2024Article
- Transcriptome-wide characterization of genetic perturbations.bioRxiv : the preprint server for biology · 2024Article
- A community effort to track commercial single-cell and spatial 'omic technologies and business trends.Nature biotechnology · 2024Article
- Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology.Biodesign research · 2024Review
- Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data.Genome biology and evolution · 2023Article
- Article
Corrections and comments
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
Abstract
Here we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology. mnSBS uses mostly natural, unmodified nucleotides and only a low fraction of fluorescently labeled nucleotides, which allows for high polymerase processivity and lower costs. We demonstrate successful application in four scRNA-seq case studies of different technical and biological types, including 5' and 3' scRNA-seq, human peripheral blood mononuclear cells from a single individual and in multiplex, as well as Perturb-Seq. Benchmarking shows that results from mnSBS-based scRNA-seq are very similar to those using Illumina sequencing, with minor differences in results related to the position of reads relative to annotated gene boundaries, owing to single-end reads of Ultima being closer to gene ends than reads from Illumina. The method is thus compatible with state-of-the-art scRNA-seq libraries independent of the sequencing technology. We expect mnSBS to be of particular utility for cost-effective large-scale scRNA-seq projects.
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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.