ReviewNature protocols2018
Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies.
Review in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- A Cell Atlas of Adult Aedes aegypti Midgut Revealed by Single Nucleus/Cell RNA Sequencing.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Single-cell and spatial transcriptomics reveals the spatiotemporal trajectory of the small peptide TAP4 in delaying postharvest fruit senescence.Plant communications · 2026Article
- Advances in sex-specific single-cell transcriptomic profiling in Parkinson's disease.Journal of Parkinson's disease · 2026Review
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Classification of indeterminate and off-target cell types within human kidney organoid differentiation.iScience · 2026Article
- SiteCELL enablesiScience · 2026Article
- Loss of miR-29a/b1 Cluster Reprograms the Tumor Microenvironment and Contributes to Immunosuppression in Lung Cancer.Cancer immunology research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Cell type-specific dissection of cell death programs during ovarian aging.Briefings in bioinformatics · 2026Article
- Whole-organism spatial transcriptomics at single-cell resolution inbioRxiv : the preprint server for biology · 2026Article
- Comprehensive guide for optimizing octopus immune cell preparation to enhance single cell RNA sequencing success.Scientific reports · 2026Article
- TRIM29 promotes pancreatic cancer MVI via IκBα K48-ubiquitination and NF-κB activation in CXCL5⁺ epithelial cells.Molecular cancer · 2026Article
- Single-cell transcriptome sequencing revealing the microenvironment of breast fibroepithelial tumor.Biochemistry and biophysics reports · 2026Article
- Charting cell-type-specific positive genetic interaction at single-cell resolution for lung adenocarcinoma.NPJ precision oncology · 2026Article
- APOE4-driven T cell dysregulation in Alzheimer's disease: single-cell genomics and Mendelian randomization reveal novel therapeutic targets.Journal of neuroinflammation · 2026Article
- Biomaterial-mediated Cell Atlas: an insight from single-cell and spatial transcriptomics.Bioactive materials · 2025Review
- Key Considerations on CITE-Seq for Single-Cell Multiomics.Proteomics · 2025Review
- Methods and applications of in vivo CRISPR screening.Nature reviews. Genetics · 2025Review
- Article
- A model for the adaptation of Euryale ferox leaves to aquatic environments through EfCGT1-controlled flavonoid C-glycoside-specific accumulation in epidermis cells.Plant biotechnology journal · 2025Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing is at the forefront of high-resolution phenotyping experiments for complex samples. Although this methodology requires specialized equipment and expertise, it is now widely applied in research. However, it is challenging to create broadly applicable experimental designs because each experiment requires the user to make informed decisions about sample preparation, RNA sequencing and data analysis. To facilitate this decision-making process, in this tutorial we summarize current methodological and analytical options, and discuss their suitability for a range of research scenarios. Specifically, we provide information about best practices for the separation of individual cells and provide an overview of current single-cell capture methods at different cellular resolutions and scales. Methods for the preparation of RNA sequencing libraries vary profoundly across applications, and we discuss features important for an informed selection process. An erroneous or biased analysis can lead to misinterpretations or obscure biologically important information. We provide a guide to the major data processing steps and options for meaningful data interpretation. These guidelines will serve as a reference to support users in building a single-cell experimental framework-from sample preparation to data interpretation-that is tailored to the underlying research context.
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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.