Size matters - the impact of nucleus size on results from spatial transcriptomics
Size matters - the impact of nucleus size on results from spatial transcriptomics
Abstract Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover novel modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei. Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on results from spatial transcriptomic study of human postmortem brains. CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain.
Davies Hanna、Kostecka Anna、Olszewski Pawe?、Chojnowska Katarzyna、Bie¨?kowski Micha?、Ingelsson Martin、Filipowicz Natalia、Wierzbicka Justyna M.、Dumanski Jan P.、Piotrowski Arkadiusz、Mieczkowski Jakub、J?kalski Marcin、Hyman Bradley T.、Koczkowska Magdalena、Mohammadi Elyas、?mijewski Micha? A.
Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University3P-Medicine Laboratory, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?skDepartment of Pathomorphology, Medical University of Gda¨?skDepartment of Public Health and Caring Sciences, Geriatrics, Rudbeck Laboratory, Uppsala University||Krembil Brain Institute, University Health Network||Department of Medicine and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto3P-Medicine Laboratory, Medical University of Gda¨?skDepartment of Histology, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?sk||Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University3P-Medicine Laboratory, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?skDepartment of Neurology, Massachusetts General Hospital||Massachusetts Alzheimer?ˉs Disease Research Center||Harvard Medical School3P-Medicine Laboratory, Medical University of Gda¨?sk3P-Medicine Laboratory, Medical University of Gda¨?skDepartment of Histology, Medical University of Gda¨?sk
基础医学生物科学研究方法、生物科学研究技术神经病学、精神病学
Davies Hanna,Kostecka Anna,Olszewski Pawe?,Chojnowska Katarzyna,Bie¨?kowski Micha?,Ingelsson Martin,Filipowicz Natalia,Wierzbicka Justyna M.,Dumanski Jan P.,Piotrowski Arkadiusz,Mieczkowski Jakub,J?kalski Marcin,Hyman Bradley T.,Koczkowska Magdalena,Mohammadi Elyas,?mijewski Micha? A..Size matters - the impact of nucleus size on results from spatial transcriptomics[EB/OL].(2025-03-28)[2025-07-02].https://www.biorxiv.org/content/10.1101/2022.03.31.486657.点此复制
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