Average Values per Cluster






Please specify the input for the Coverage Plot here. The input from the left panel is not considered.


Download Plot






Seurat object - atlas.RDS
Metadata - atlas-metadata.tsv
Fragment files - fragments.tar
List of identified peaks - atlas_clustpeaks.features.txt
List of JASPAR motifs (2024) - motif-id-name.db.tsv
Gene activity (promoter length 500 bp) per cluster - atlas_activity_500.cluster-average.txt
Gene activity (promoter length 1000 bp) per cluster - atlas_activity_1000.cluster-average.txt
Gene activity (promoter length 3000 bp) per cluster - atlas_activity_3000.cluster-average.txt
Motif activity per cluster - atlas_chromvar.cluster-average.txt
Chromatin (peak) accessibility per cluster - atlas_clustpeaks.cluster-average.txt



Average Values per Cluster






Please specify the input for the Coverage Plot here. The input from the left panel is not considered.


Download Plot






Seurat object - cortex.RDS
Metadata - cortex-metadata.tsv
Fragment files - fragments.tar
List of identified peaks - atlas_clustpeaks.features.txt
List of JASPAR motifs (2024) - motif-id-name.db.tsv
Gene activity (promoter length 500 bp) per cluster - cortex_activity_500.cluster-average.txt
Gene activity (promoter length 1000 bp) per cluster - cortex_activity_1000.cluster-average.txt
Gene activity (promoter length 3000 bp) per cluster - cortex_activity_3000.cluster-average.txt
Motif activity per cluster - cortex_chromvar.cluster-average.txt
Chromatin (peak) accessibility per cluster - cortex_clustpeaks.cluster-average.txt



Average Values per Cluster






Please specify the input for the Coverage Plot here. The input from the left panel is not considered.


Download Plot






Seurat object - endo.RDS
Metadata - endo-metadata.tsv
Fragment files - fragments.tar
List of identified peaks - atlas_clustpeaks.features.txt
List of JASPAR motifs (2024) - motif-id-name.db.tsv
Gene activity (promoter length 500 bp) per cluster - endo_activity_500.cluster-average.txt
Gene activity (promoter length 1000 bp) per cluster - endo_activity_1000.cluster-average.txt
Gene activity (promoter length 3000 bp) per cluster - endo_activity_3000.cluster-average.txt
Motif activity per cluster - endo_chromvar.cluster-average.txt
Chromatin (peak) accessibility per cluster - endo_clustpeaks.cluster-average.txt

User Manual



1. Provided Data

  • The provided dataset was originally published in Denyer and Solansky et al. (2026).
  • This dataset comprises single-cell ATAC-seq data from the Arabidopsis root tip, representing an atlas that captures chromatin accessibility across all principal cell types of the tissue.
  • Special emphasis was placed on the fine curation and detailed annotation of cortex and endodermis cell files. These two isolated sub-datasets are provided and can be selected in the upper navigation bar.
  • Please refer to the publication for more information about the data.



2. Browsable Features

    • 1. Gene Activity – Quantification of chromatin accessibility associated with a gene promoter. It may be used for indirect estimation of gene expression. It is calculated as a sum of fragments that have been mapped to the promoter region of a queried gene. The promoter length can be specified as 500, 1000, and 3000 bp upstream of the TSS. Note that gene activity tends to be much noisier than scRNA-seq data due to data sparsity and the assumption of correspondence of promoter accessibility and gene expression, which may not always be the case.

    • 2. Motif Accessibility – Quantification of TF-associated chromatin accessibility variability across cells, calculated with the chromVAR package. In other words, it estimates motif activity enrichment by quantifying accessibility deviations at the TF binding regions. This function is useful for estimating TF/TF family employment (‘importance’) in various cell types.

    • 3. Identified Peaks – This feature allows for visualization of the accessibility of specified peaks across the atlas. The valid input is the previously identified peaks. The list of all identified peaks can be obtained in the Downloads section or from the Coverage Plot tab (see below). This function can be useful in case the user is interested in a specific peak, for instance, in a promoter of a gene of interest. The browser uses the JASPAR (2024) motif database.

    • 4. Genome Coverage – allows for plotting the frequency of Tn5 integration across regions of the genome for cell clusters. It shows pseudo-bulk accessibility tracks per cluster, similar to the standard visualization of bigwig or bedgraph files. Genome annotation and identified peaks within the plotted regions are displayed below the coverage tracks.



3. Querying Features

  • The features can be queried using the text input box on the left panel. Multiple comma-separated features can be queried.
  • Alternatively, the user can upload a simple .txt file containing one feature per line.
  • Please note that querying a large number of features can lead to slow processing. The input is currently limited to 20 features.
  • The desired feature type for plotting can be selected in the drop-down menu in the left panel.

    • The accepted input forms are:

    • 1. Gene Activity – TAIR IDs (AT5G15290…) or common gene names (SHR, SCR…). If the common gene name refers to multiple unique TAIR IDs, please use the TAIR ID instead. The promoter length can be specified in the left panel. Changing promoter length affects only Gene activity.

    • 2. Motif Accessibility – JASPAR motif ID (MA1015.2) or motif name (GATA12). If the JASPAR ID without the last digit (.1, .2) is inserted, all corresponding motif versions will be plotted.

    • 3. Identified Peaks – The only accepted input are the peak names present in the atlas_clustpeaks.features.txt file that is available in the Downloads section. The input must be strictly in form chr-start-end (hyphen-separated).

    • 4. Genome Coverage – This functionality can be found in a tab ‘Coverage Plot’ which contains a separate input form. The region to visualize is specified as ‘chr-start-end’ (hyphen-separated) or as a TAIR IDs . Only a single region can be queried at time. The defined region must not span more than 15 kb. Additionally, the user can specify upstream and downstream extensions up to 5 kb each. This is useful when plotting genes since the accessible chromatin regions are often expected upstream of the gene body.

  • A table with plotted IDs and corresponding names is shown in the top screen part, allowing simple linkage of plotted features to their names.
  • If the queried features are not present in the dataset, an error notification will be displayed in the bottom-right screen corner, and the feature will not appear in the output plot.
  • If the common name is used and not found, please doublecheck with ID.



4. Feature Plot

  • The feature plot shows the normalized values of individual cells (dots) projected on a UMAP visualization. A more intense red color means a higher activity/accessibility.
  • Each plot has an individual scale. Therefore, the expression levels of individual genes cannot be directly compared using the color intensities without considering the scale bar.
  • For interpretation of observed expression patterns, please refer to the cluster legend on the left panel.



5. Cluster Values

  • The violin plots show the normalized values of the cells (dots) within individual clusters.
  • In the case of low activity/accessibility, the violin plots can look like lines. This is an expected behavior due to many cells (dots) accumulated at zero values.
  • The average values per cell cluster can be browsed in the Average Cluster Values tab.



6. Coverage Plot

  • The Coverage Plot tab allows for genome coverage visualization. The input for this functionality is separated from the inputs for the other visualization features.
  • Maximum 15 kb region + 5 kb extensions can be plotted



7. Developmental Trajectories

  • Additionally, the browser allows for the visualization of feature activity/accessibility across the developmental trajectories of cortex and endodermis (select in the upper bar).
  • The dynamics over the tissue developmental trajectory can be explored at the ‘Trajectory Plot’ and ‘Trajectory Heatmap’ sections.
  • The individual cells are ordered based on pseudotime values, representing a developmental continuum.
  • The identities of cells in different trajectory regions and pseudotime values are indicated on the color bar on the top.
  • The 'Trajectory Plot’ shows the activity/accessibility values of individual cells and a smooth expression trend as a fitted cubic spline over the pseudotime. This plot is useful for plotting the expression dynamics of individual or a small number of genes.
  • The ‘Trajectory Heatmap’ shows the smooth fitted curve in the form of a heatmap. This visualization is useful for exploring a larger number of genes.



8. Data Download

  • Seurat object – a fully processed Seurat object (.RDS). It contains a 'ATAC' assay used for initial clustering, and 'clustpeaks' assay used for downstream analyses.
  • Metadata – a cell-level metadata extracted from the Seurat object.
  • Fragments – fragment files generated by CellRanger. These are shared between atlas, cortex, and endodermis objects.
  • List of identified peaks – a list of the identified peaks. The peak names from this file are valid input for querying Identified Peaks.
  • List of JASPAR motifs (2024) – a list of the motifs from JASPAR database (2024) that can be queried. Also contains the corresponding motif names.
  • Gene activity (…) per cluster – The average values for cell clusters.
  • Motif activity per cluster – The average values for cell clusters.
  • Chromatin (peak) accessibility per cluster – The average values for cell clusters.



9. Citation



    10. Contact

    • If you have any questions, please contact: marja.timmermans@zmbp.uni-tuebingen.de
    • If you wish to report a bug in the browser, please contact Pavel Solanský: pavel.solansky@zmbp.uni-tuebingen.de

    • Timmermans Lab