Arabidopsis Developmental Atlas Viewer

Profiling the transcriptomes of single-cells along the entire lifecycle of Arabidopsis

Incredible tissue diversity exists throughout Arabidopsis development; from seeds to, roots, leaves, stems, and reproductive tissues, and the composition and arrangement of cells and cell types within. To survey cell type diversity throughout development, we applied single-nucleus RNA sequencing to whole tissues and organs at ten distinct developmental timepoints, resulting in over 400,000 stringently filtered nuclei and 183 clusters.

This browser enables the exploration of each of our single nucleus transcriptome datasets, and may serve as a reference for cell type specific and developmental specific expression of genes throughout the entirety of Arabidopsis lifecycle.

For a brief tutorial on data exploration click here

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

Access the preprint at:

Basic CELLxGENE tutorial

Input your gene of interest into the field and click button indicated to color by your gene of interest. Scaled expression values of the all transcripts are displayed.

Click here to color the graph by cluster number

Click here to color the graph by cell type annotation

For a more in-depth CELLxGENE resources visit CELLxGENE


Raw sequencing data and processed data are available at GEO accession: GSE226097

Spatial imaging data can be found here
To interact with the processed data download the Vizgen Visualizer software


Interactive data browsing utilizes CELLxGENE

Dataset serving utilizes CELLxGENE-gateway


The Arabidopsis developmental atlas is maintained by Travis Lee


August 30, 2023

Now browse the normalized expression of all transcripts detected within each dataset.

July 12, 2023

Find the processed silique MERFISH dataset here
To interact with the processed data download the Vizgen Visualizer software

March 30, 2023

We are live! Interact and browse the expression of up to 2,000 of the highly variable genes identified in each of the 11 individual datasets and the integrated rosette and seedling time course datasets.