ArticleNature protocols2019
MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers, 1 of them a synthesis that pooled it.
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
160 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Single-cell RNA sequencing offers novel perspectives in viral infection research.Frontiers in cellular and infection microbiology · 2026Pooled it
- Single-cell RNA sequencing unravels mosquito biology and host-pathogen interactions.Parasites & vectors · 2026Review
- Reciprocal, methylation-dependent binding of Zfp57 and Gzf1 safeguards Dlk1-Dio3 imprinting during developmental reprogramming.Nature communications · 2026Article
- Spatially Resolved ABA Signalling Reveals Dual Role in Tomato Yield.Plant biotechnology journal · 2026Article
- Diversity and evolution of chromatin regulatory states across eukaryotes.Nature genetics · 2026Article
- A single-cell atlas of multiple myeloma defines malignant archetypes and proliferative states.Nature genetics · 2026Article
- An endometrial immune atlas across the female menstrual cycle reveals lymphoid aggregates compromise pregnancy.Nature communications · 2026Article
- Unexpected Suppression of Tomato Fruit Cuticle Formation by Overexpression of a Key Cutin Biosynthetic Enzyme.Plant biotechnology journal · 2026Article
- Hypoglycemic conditions enhance neonatal β-cell glucose responsiveness via AMPK/mTOR-increased KATP channel density.Endocrinology · 2026Article
- A conserved biphasic venous remodeling program governs inferior vena cava formation in zebrafish.Science advances · 2026Article
- IRE1-XBP1driven induction of TMED9 stabilizes ATF6 during ER stress to promote cell survival.Cellular & molecular biology letters · 2026Article
- Lysosome-related organelles orchestrate guanine crystal formation in pigment cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Features affecting Cas9-induced editing efficiency and patterns in tomato: evidence from a large CRISPR dataset.The Plant journal : for cell and molecular biology · 2026Article
- Pleiotropic mutation in a tendril TCP gene underlies the yield-enhancing multiple-flowering trait in summer squash (Cucurbita pepo).The Plant journal : for cell and molecular biology · 2026Article
- GeneExt: a gene model extension tool for enhanced single-cell RNA-seq analysis.Bioinformatics (Oxford, England) · 2026Article
- Cellular and transcriptional trajectories of neural fate specification in sea anemone uncover two modes of adult neurogenesis.Nature communications · 2026Article
- AI-Based Prediction of Gene Expression in Single-Cell and Multiscale Genomics and Transcriptomics.International journal of molecular sciences · 2026Review
- Advances in single-cell transcriptomic sequencing in hepatic echinococcosis.Frontiers in immunology · 2026Review
- Heterogeneity and characteristic changes in cardiomyocytes and non‑cardiomyocytes following myocardial infarction: Insights from single‑cell sequencing analysis (Review).Molecular medicine reports · 2025Review
- Article
100 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human tissues comprise trillions of cells that populate a complex space of molecular phenotypes and functions and that vary in abundance by 4-9 orders of magnitude. Relying solely on unbiased sampling to characterize cellular niches becomes infeasible, as the marginal utility of collecting more cells diminishes quickly. Furthermore, in many clinical samples, the relevant cell types are scarce and efficient processing is critical. We developed an integrated pipeline for index sorting and massively parallel single-cell RNA sequencing (MARS-seq2.0) that builds on our previously published MARS-seq approach. MARS-seq2.0 is based on >1 million cells sequenced with this pipeline and allows identification of unique cell types across different tissues and diseases, as well as unique model systems and organisms. Here, we present a detailed step-by-step procedure for applying the method. In the improved procedure, we combine sub-microliter reaction volumes, optimization of enzymatic mixtures and an enhanced analytical pipeline to substantially lower the cost, improve reproducibility and reduce well-to-well contamination. Data analysis combines multiple layers of quality assessment and error detection and correction, graphically presenting key statistics for library complexity, noise distribution and sequencing saturation. Importantly, our combined FACS and single-cell RNA sequencing (scRNA-seq) workflow enables intuitive approaches for depletion or enrichment of cell populations in a data-driven manner that is essential to efficient sampling of complex tissues. The experimental protocol, from cell sorting to a ready-to-sequence library, takes 2-3 d. Sequencing and processing the data through the analytical pipeline take another 1-2 d.
Indexed as
Identifiers
31101904What 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.