ArticleNature communications2020
Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 2 of them syntheses that pooled it.
What it found
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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
44 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A resource for integrated genomic analysis of the human liver.Scientific reports · 2022Pooled it
- Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits.Nature genetics · 2022Pooled it
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- eQTL analysis: A bridge from genome to mechanism.Genes & diseases · 2026Review
- scMILD: Single-cell multiple instance learning for sample classification and associated subpopulation discovery.iScience · 2026Article
- Single-cell and spatial profiling in cancer biology and clinical oncology.Nature cancer · 2026Review
- Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression.bioRxiv : the preprint server for biology · 2026Article
- Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology.bioRxiv : the preprint server for biology · 2026Article
- Detecting chromatin state alterations in PBMCs associated with Type 2 Diabetes Mellitus.Communications medicine · 2026Article
- scDesignPop generates realistic population-scale single-cell RNA-seq for power analysis, benchmarking, and privacy protection.bioRxiv : the preprint server for biology · 2026Article
- Article
- Spatially resolved gene expression analysis illuminates location-specific functions in the reef-building coral Pocillopora acuta.PloS one · 2026Article
- Unravelling the pathogenic mechanisms in Graves' orbitopathy.European thyroid journal · 2025Review
- Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux.bioRxiv : the preprint server for biology · 2025Article
- Single cell RNA-sequencing identified CCR7+/RELB+/IRF1+ T cell responding for juvenile idiopathic arthritis pathogenesis.Frontiers in immunology · 2025Article
- Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders.American journal of human genetics · 2024Article
- eQTL studies: from bulk tissues to single cells.Journal of genetics and genomics = Yi chuan xue bao · 2023Review
- Single-cell transcriptomics of the ocular anterior segment: a comprehensive review.Eye (London, England) · 2023Review
- Methods and Insights from Single-Cell Expression Quantitative Trait Loci.Annual review of genomics and human genetics · 2023Review
- ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool in population-scale analyses, due to its prohibitively high cost. Here we show that given the same budget, the statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping can be increased through low-coverage per-cell sequencing of more samples rather than high-coverage sequencing of fewer samples. We use simulations starting from one of the largest available real single-cell RNA-Seq data from 120 individuals to also show that multiple experimental designs with different numbers of samples, cells per sample and reads per cell could have similar statistical power, and choosing an appropriate design can yield large cost savings especially when multiplexed workflows are considered. Finally, we provide a practical approach on selecting cost-effective designs for maximizing cell-type-specific eQTL power which is available in the form of a web tool.
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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.