Spatial Transcriptomics correlated Electron Microscopy MERFISH and scRNA-Seq Version 1
External LinkCurrent spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden foamy microglia to transcriptional signature. Moreover, we revealed that interferon-response microglia have unique morphology and are enriched near CD8 T-cells.
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Created: 27th Jun 2024 at 12:05
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Version 1 (earliest) Created 27th Jun 2024 at 12:05 by Rainer Malik
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Projects: SyNergy - published datasets
Institutions: Klinikum der Universität München
Public web page: Not specified
Submitter: Rainer Malik
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Assays: Bulk RNA-seq, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Single cell RNA sequencing experiment, scRNA-seq 5 day, scRNA-seq day 20
Submitter: Rainer Malik
Investigation: Transcriptomics
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Transcriptomics
Abstract (Expand)
Authors: P. Androvic, M. Schifferer, K. Perez Anderson, L. Cantuti-Castelvetri, H. Jiang, H. Ji, L. Liu, G. Gouna, S. A. Berghoff, S. Besson-Girard, J. Knoferle, M. Simons, O. Gokce
Date Published: 11th Jul 2023
Publication Type: Journal
