ArticleNature methods2021
Joint single-cell measurements of nuclear proteins and RNA in vivo.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 2 of them syntheses that pooled it.
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Who cites it
86 citing papers in PubMed, 2 syntheses or guidelines pooled it, 130 citations in OpenAlex.
- Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data.Genome biology · 2023Pooled it
- Integration ofFrontiers in immunology · 2023Pooled it
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- Single-cell transcriptomic atlas of frontoinsular cortex reveals molecular correlates of selective neuronal vulnerability in FTD.bioRxiv : the preprint server for biology · 2026Article
- Aging disrupts spatiotemporal coordination in the cycling murine ovary.Nature aging · 2026Article
- Robust integration of single-cell datasets with imbalanced modality composition.Nature communications · 2026Article
- Disordered protein LAT encodes relative levels of signaling pathways in T cell activation.Science (New York, N.Y.) · 2026Article
- Machine learning predictions surpass individual mRNAs as a proxy of single-cell protein expression.Genome biology · 2026Article
- Integrating MACSPI and SILAC for Neuron Type-specific Proteomics in Caenorhabditis elegans.Molecular & cellular proteomics : MCP · 2026Article
- SCITO-seq2: ultra-high-throughput single-cell transcriptome and epitope sequencing.Genome biology · 2026Article
- Idiopathic Pulmonary Fibrosis: Cellular Heterogeneity, Mechanisms, and Therapeutic Implications.MedComm · 2025Review
- Key Considerations on CITE-Seq for Single-Cell Multiomics.Proteomics · 2025Review
- Cassini: streamlined and scalable method for in situ profiling of RNA and protein.Nature communications · 2025Article
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- Single-cell epigenomics and proteomics methods integrated in multiomics.Fundamental research · 2025Review
- Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators.bioRxiv : the preprint server for biology · 2025Article
- Integration of phospho-signaling and transcriptomics in single cells reveals distinct Th17 cell fates.Cell reports · 2025Article
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment.Molecular cancer · 2025Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
Identifying gene-regulatory targets of nuclear proteins in tissues is a challenge. Here we describe intranuclear cellular indexing of transcriptomes and epitopes (inCITE-seq), a scalable method that measures multiplexed intranuclear protein levels and the transcriptome in parallel across thousands of nuclei, enabling joint analysis of transcription factor (TF) levels and gene expression in vivo. We apply inCITE-seq to characterize cell state-related changes upon pharmacological induction of neuronal activity in the mouse brain. Modeling gene expression as a linear combination of quantitative protein levels revealed genome-wide associations of each TF and recovered known gene targets. TF-associated genes were coexpressed as distinct modules that each reflected positive or negative TF levels, showing that our approach can disentangle relative putative contributions of TFs to gene expression and add interpretability to inferred gene networks. inCITE-seq can illuminate how combinations of nuclear proteins shape gene expression in native tissue contexts, with direct applications to solid or frozen tissues and clinical specimens.
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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.