About
Spatial
Mock 4hr AvrRpt2 6hr AvrRpt2 9hr AvrRpt2 24hr AvrRpt2 24hr DC3000 All Spatial
snMultiome
Mock 4hr AvrRpt2 6hr AvrRpt2 9hr AvrRpt2 24hr AvrRpt2 24hr DC3000 All Multiome
Joint Embedding
Joint Mock Joint 4hr AvrRpt2 Joint 6hr AvrRpt2 Joint 9hr AvrRpt2 Joint 24hr AvrRpt2 Joint 24hr DC3000
Information
Tutorial Data Documentation Contact Changelog

Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack

Plant leaf intercellular space provides a nutrient-rich and heterogeneous niche for microbes that critically impacts plant health. However, how individual plant cells respond to heterogeneous microbial colonization remains largely elusive. Here, by time-resolved simultaneous single-cell transcriptome and epigenome profiling of plants (Arabidopsis thaliana) infected by virulent and avirulent bacterial pathogens (Pseudomonas syringae), we present cell atlases with gene regulatory logic involving transcription factors, putative cis-regulatory elements, and target genes associated with disease and immunity. We also identify previously uncharacterized cell populations with distinct immune gene expression within major developmental cell types. Furthermore, we employ time-resolved spatial transcriptomics to reveal spatial heterogeneity of plant immune responses linked to pathogen distribution. Integrating our single-cell multiomics and spatial omics data enables spatiotemporal mapping of defense gene regulatory logic with pathogen cells. Our study provides a molecularly-defined spatiotemporal map of plant-microbe interaction at the single-cell resolution.

If you have any trouble exploring our datasets using the CellxGene Gateway, visit here

Notice: when accessing larger datasets, it may take several minutes to load the dataset

Spatial Experimental Design

Spatial Protocol Image

Single Nucleus Multiome Experimental Design

Seq Protocol Image

Spatial Experiments - Click to browse

Single Nucleus Multiome Experiments

Joint Embeddings

Access the preprint at:

Welcome to the CELLxGENE Tutorial

After clicking on an experiment to browse with cellxgene:

Adjusting expression values for visualization: There are two ways to do this (1) entering min/max values for clipping and (2) select a range on a histogram. One can combine these two approaches to adjust visualization.

Display Gene Expression: Look up a gene name in the top right of the frame. Click on the expand button and adjust the min and max expression values.

ATAC Counts or Chromvar Motif Enrichment: In the gene search bar type ATAC_{name of gene} or Chromvar_{name of gene respectively}.

Change Projection: To change the projection (e.g., Spatial, UMAP, Joint spatial UMAP), click the rectangular bottom left button.

Display Categorical Variable: Click the color button next to the variable of interest on the left pane.

Display Continuous Variable: Find it in the left pane, color the plot, and adjust the range.

For in-depth CELLxGENE instructions visit CELLxGENE

Data
Raw sequencing data, processed data, and imaging data are available by request.

Documentation
Interactive data browsing utilizes CELLxGENE

Dataset serving utilizes CELLxGENE-gateway

Contact

This spatial-temporal Arabidopsis pathogen atlas is maintained by Alexander Monell and Tatsuya Nobori

Changelog
12-03-2023 Website Launched.