ArticleeLife2025
Spatial transcriptomics in the adult
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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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
6 citing papers in PubMed.
- Connectivity of serotonin neurons reveals a constrained inhibitory subnetwork within the olfactory system.Journal of neurophysiology · 2026Article
- Bridges under construction: the dynamics of ring canal expansion during Drosophila oogenesis.Developmental biology · 2026Review
- Modern Mining: The Role of Single-cell RNA Sequencing in Advancing Neuroscience Research.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Emerging tools to advance neuroethology in butterflies and moths.Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology · 2026Review
- From candidate genes to omics: Unbiased approaches reshaping arthropod Evo-Devo.Genetics and molecular biology · 2026Article
- Single-cell transcriptional landscapes of Aedes aegypti midgut and fat body after a bloodmeal.Cell genomics · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
Recently, we have achieved a significant milestone with the creation of the Fly Cell Atlas. This single-nuclei atlas encompasses the entire fly, covering the entire head and body, in addition to all major organs. This atlas catalogs many hundreds of cell types, of which we annotated 250. Thus, a large number of clusters remain to be fully characterized, in particular in the brain. Furthermore, by applying single-nuclei sequencing, all information about the spatial location of the cells in the body and of about possible subcellular localization of the mRNAs within these cells is lost. Spatial transcriptomics promises to tackle these issues. In a proof-of-concept study, we have here applied spatial transcriptomics using a selected gene panel to pinpoint the locations of 150 mRNA species in the adult fly. This enabled us to map unknown clusters identified in the Fly Cell Atlas to their spatial locations in the fly brain. Additionally, spatial transcriptomics discovered interesting principles of mRNA localization and transcriptional diversity within the large and crowded muscle cells that may spark future mechanistic investigations. Furthermore, we present a set of computational tools that will allow for easier integration of spatial transcriptomics and single-cell datasets.
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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.