Abstract
Single-cell or single-nucleus transcriptomics is a powerful tool for identifying cell types and cell states. However, hypotheses derived from these assays, including gene expression information, require validation, and their functional relevance needs to be established. The choice of validation depends on numerous factors. Here, we present types of orthogonal and functional validation experiment to strengthen preliminary findings obtained using single-cell and single-nucleus transcriptomics as well as the challenges and limitations of these approaches.
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Acknowledgements
We thank I. Adameyko, T. Bakken, A. Bhaduri, B. Bonev, G. Castelo-Branco, F. Chen, C. Chhatbar, S. Codeluppi, R. Corces, J. Fan, M. G. Filbin, D. Gate, G. Green, M. Heiman, K. Harris, H. Hochgerner, F. Inoue, M. Kellis, C. N. Kim, J. Krull, G. L. Manno, A. Levine, Q. Li, S. Linnarsson, M. Lotfollahi, C. Luo, Q. Ma, E. Macosko, C. Mayer, K. R. Maynard, V. Menon, P. Nano, M. Nitzan, M. Prinz, S. Quake, V. Ramani, R. Satijia, L. Schirmer, Y. Shen, N. Sun, F. Theis, C. Walsh, X. Wang, J. D. Welch and J. Yang for the insightful feedback on this work. M.C. thanks A. U. Antonova for helpful additional discussions. G.K. is a Jon Heighten Scholar in Autism Research and Townsend Distinguished Chair in Research on Autism Spectrum Disorders at UT Southwestern, and was partially supported by the James S. McDonnell Foundation 21st Century Science Initiative in Understanding Human Cognition Scholar Award (220020467), Simons Foundation for Autism Research Award (947591) and National Institutes of Health (NIH) grants (NS126143, HG011641, MH126481, NS115821). S.A.L. is supported by the Carol and Gene Ludwig Family Foundation, The Cure Alzheimer’s Fund, the National Multiple Sclerosis Society and NIH grants (R01EY033353, R03NS127079). C.R.C. is supported by the Weill Neurohub, the Shurl and Kay Curci Foundation, the CURE Epilepsy Taking Flight Award and grants from the NIH (K08NS126573, U01NS132353). E.C. is a Neural Scientist Training Program Fellow in the Peter O’Donnell Brain Institute at UT Southwestern. J.L.C. is supported by NIH grant U01MH10907. J.G. is supported by NIH grant R01MH113005. M.S. is supported by a HHMI Hanna H. Gray Fellowship, a SFARI Pilot Award and a NYSCF Druckenmiller Fellowship. J.W. is supported by NIH grant R01MH113005. M.E.U. is supported by the National Science Foundation Graduate Research Fellowship Program and a Hertz Foundation Fellowship Program.
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M.C. is a member of the Scientific Advisory Board of Vigil, NGMBio, Cartesian and Halyardtx. M.C. receives research support from Ono Pharmaceutical, is a consultant for CST and has patents pending on LILRB4 and TREM2. S.A.L. maintains a financial interest in AstronauTx and Synapticure and is on the Scientific Advisory Board of the Global BioAccess Fund. S.A.L. is an inventor on US Patents WO2018081250A1 and WO2022187517A1. M.K. is a co-scientific founder of Montara Therapeutics and serves on the Scientific Advisory Boards of Engine Biosciences, Casma Therapeutics, Cajal Neuroscience, Alector and Montara Therapeutics, and is an advisor to Modulo Bio and Recursion Therapeutics. M.K. is an inventor on US Patent 11,254,933 related to CRISPRi and CRISPRa screening, and on a US Patent Application on in vivo screening methods. All other authors declare no competing interests.
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Colonna, M., Konopka, G., Liddelow, S.A. et al. Implementation and validation of single-cell genomics experiments in neuroscience. Nat Neurosci 27, 2310–2325 (2024). https://doi.org/10.1038/s41593-024-01814-0
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DOI: https://doi.org/10.1038/s41593-024-01814-0
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