ArticleGenome biology2020
Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Single-Cell Meta-Analysis Uncovers the Pancreatic Endothelial Cell Transcriptomic Signature and Reveals a Key Role for NKX2-3 in PLVAP Expression.Arteriosclerosis, thrombosis, and vascular biology · 2024Pooled it
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- Resolving human α versus β cell fate allocation for the generation of stem cell-derived islets.Nature communications · 2026Article
- Long QT syndrome and hypoglycemia in a postbariatric surgery patient with a likely pathogenic variant inJCEM case reports · 2026Article
- The molecular mechanisms of incretin resistance in Type 2 Diabetes Mellitus (T2DM).Nutrition & diabetes · 2026Review
- Investigational treatments of β-cell failure and replacement.Diabetology international · 2026Review
- Benchmarking computational decontamination of ambient RNA.Frontiers in bioinformatics · 2026Article
- α-cell SLC38A5 supports amino acid-induced α-cell proliferation and glucagon secretion.Frontiers in endocrinology · 2026Article
- The contrasting effects of two antimalarial drugs on insulin secretion.Cellular and molecular life sciences : CMLS · 2025Article
- Drug Search and Design Considering Cell Specificity of Chemically Induced Gene Expression Profiles for Disease-Associated Tissues.Molecular informatics · 2025Article
- Alleviating batch effects in cell type deconvolution with SCCAF-D.Nature communications · 2024Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data.Genome biology · 2024Article
- Follicle-stimulating hormone orchestrates glucose-stimulated insulin secretion of pancreatic islets.Nature communications · 2023Article
- Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas.Nature metabolism · 2023Article
- Biologically informed deep learning to query gene programs in single-cell atlases.Nature cell biology · 2023Article
- Transcriptional signature of islet neogenesis-associated protein peptide-treated rat pancreatic islets reveals induction of novel long non-coding RNAs.Frontiers in endocrinology · 2023Article
- Artemether treatment improves islet function and metabolic homeostasis in diabetic nonhuman primates.Journal of diabetes · 2023Article
- Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing.Nature communications · 2022Article
- Challenges in translational machine learning.Human genetics · 2022Review
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 at 5 institutions in 2 countries.
Funding
Abstract
backgroundSingle-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-specific effects of drug treatment in complex tissues. This application requires high levels of precision, robustness, and quantitative accuracy-beyond those achievable with existing methods for mainly qualitative single-cell analysis. Here, we establish the use of standardized reference cells as spike-in controls for accurate and robust dissection of single-cell drug responses.
resultsWe find that contamination by cell-free RNA can constitute up to 20% of reads in human primary tissue samples, and we show that the ensuing biases can be removed effectively using a novel bioinformatics algorithm. Applying our method to both human and mouse pancreatic islets treated ex vivo, we obtain an accurate and quantitative assessment of cell-specific drug effects on the transcriptome. We observe that FOXO inhibition induces dedifferentiation of both alpha and beta cells, while artemether treatment upregulates insulin and other beta cell marker genes in a subset of alpha cells. In beta cells, dedifferentiation and insulin repression upon artemether treatment occurs predominantly in mouse but not in human samples.
conclusionsThis new method for quantitative, error-correcting, scRNA-seq data normalization using spike-in reference cells helps clarify complex cell-specific effects of pharmacological perturbations with single-cell resolution and high quantitative accuracy.
Indexed as
Identifiers
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.