Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap
TL;DR: In this paper , a multiplexed fluorescence in situ hybridization method is proposed to enable single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost.
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Abstract: Retrieving the complex responses of individual cells in the native three-dimensional tissue context is crucial for a complete understanding of tissue functions. Here, we present PHYTOMap (plant hybridization-based targeted observation of gene expression map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. We applied PHYTOMap to simultaneously analyse 28 cell-type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-sequencing datasets in complex plant tissue.
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References
Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography
TL;DR: New results are derived on the minimum number of landmarks needed to obtain a solution, and algorithms are presented for computing these minimum-landmark solutions in closed form that provide the basis for an automatic system that can solve the Location Determination Problem under difficult viewing.
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.
SCANPY: large-scale single-cell gene expression data analysis
TL;DR: This work presents Scanpy, a scalable toolkit for analyzing single-cell gene expression data that includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks, and AnnData, a generic class for handling annotated data matrices.
Three-dimensional intact-tissue sequencing of single-cell transcriptional states.
Xiao Wang,William E. Allen,Matthew Wright,Emily L. Sylwestrak,Nikolay Samusik,Sam Vesuna,Kathryn E. Evans,Cindy Zang Liu,Charu Ramakrishnan,Jia Liu,Garry P. Nolan,Felice-Alessio Bava,Karl Deisseroth,Karl Deisseroth +13 more
TL;DR: An efficient sequencing approach with hydrogel-tissue chemistry was combined to develop a multidisciplinary technology for three-dimensional (3D) intact-tissues RNA sequencing and widespread up-regulation of activity-regulated genes was observed in response to visual stimulation.
1.3K
Exploring tissue architecture using spatial transcriptomics.
TL;DR: Spatial transcriptomics can also be used for hypothesis testing using experimental designs that compare time points or conditions, including genetic or environmental perturbations as mentioned in this paper, and is naturally amenable to integration with other data modalities, providing an expandable framework for insight into tissue organization.
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