ArticleNature biotechnology2020
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 545 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
545 citing papers in PubMed, 935 citations in OpenAlex.
- Leveraging Single-Cell RNA Sequencing to Characterize Murine Ewing Sarcoma Xenografts.Methods in molecular biology (Clifton, N.J.) · 2027Article
- A Cell Atlas of Adult Aedes aegypti Midgut Revealed by Single Nucleus/Cell RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Insulin receptor signaling in gustatory cells suppresses sugar taste sensitivity and feeding iniScience · 2026Article
- Peripheral somatostatin-expressing neurons are analgesic targets for refractory occipital neuralgia.Acta pharmacologica Sinica · 2026Article
- Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework.Genome research · 2026Article
- Selective depletion of upper-layer somatostatin interneuron subtypes in schizophrenia.bioRxiv : the preprint server for biology · 2026Article
- An integrated reference atlas of human skeletal muscle.EBioMedicine · 2026Article
- Distinct single-nucleus RNA-seq changes among non-neuronal cells in ADNC, LATE-NC, and mixed pathologies.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Single-cell RNA sequencing: a powerful tool to study heterogeneity in papillary and anaplastic thyroid carcinoma.European thyroid journal · 2026Review
- Single-nucleus RNA-seq and ATAC-seq analyses provide molecular insights into cadmium-stress response in alfalfa roots.Horticulture research · 2026Article
- ScanNet: Single-cell annotation informed by transcriptional regulation Network via iterative heterogeneous graph learning.PLoS computational biology · 2026Article
- A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well SNature protocols · 2026Review
- Decoding Cardiac Development and Maturation at Single-Cell and Spatial Transcriptomic Resolution.Circulation research · 2026Review
- Unifying multimodal single-cell data with a mixture-of-expertsbioRxiv : the preprint server for biology · 2026Article
- Analytical Methods and Application of Single-Cell and Single-Nucleus Transcriptomics in the Study of Ischemic Stroke.Biomolecules · 2026Review
- Single-cell transcriptomic unveils tumor-mediated reprogramming of neutrophils and their unique vulnerability that inhibits metastasis.Science advances · 2026Article
- The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.Cell genomics · 2026Article
- Single-nucleus RNA sequencing identifies conserved structural cell programs in allergic lung inflammation.The journal of allergy and clinical immunology. Global · 2026Article
- A Simple, Cost-Effective, High-Throughput Method for Measuring Chromatin Accessibility and Gene Expression in Single Nuclei.bioRxiv : the preprint server for biology · 2026Article
485 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
22 authors at 2 institutions in 1 country.
Funding
Abstract
The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single-cell and/or single-nucleus profiling-selecting representative methods based on their usage and our expertise and resources to prepare libraries-including two low-throughput and five high-throughput methods. We tested the methods on three types of samples: cell lines, peripheral blood mononuclear cells and brain tissue, generating 36 libraries in six separate experiments in a single center. To directly compare the methods and avoid processing differences introduced by the existing pipelines, we developed scumi, a flexible computational pipeline that can be used with any single-cell RNA-sequencing method. We evaluated the methods for both basic performance, such as the structure and alignment of reads, sensitivity and extent of multiplets, and for their ability to recover known biological information in the samples.
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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.