Introduction

This Shiny app provides an interactive exploration of data described in Evolutionary Rewiring of Root Cell-Type Nitrogen Responses .

Use the Arabidopsis, Tomato, and Comparison tabs above to explore the single-cell RNA-seq, bulk RNA-seq, and proteomics results.

Data Availability
  • Sequencing data: European Nucleotide Archive projects PRJEB113797 and PRJEB114121 .
  • Raw proteomics data: ProteomeXchange Consortium via the PRIDE partner repository, dataset PXD079778 .
Contact

Questions or errors? Email: zd250 [at] cam.ac.uk 🐼


One block of panels per selected genotype.
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Nitrate response DE (10mM vs 1mM).

Per-cell-type log2 fold change (10mM vs 1mM). * p<0.05, ** p<0.01, *** p<0.001
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Bulk RNA-seq: Col0 nitrate response (10mM vs 1mM). Dashed lines = |log2FC| threshold.


Bar = mean; error bars = SE; points = individual replicates.
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FeaturePlot on UMAP embedding (all conditions pooled).
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Nitrate response DE (10mM vs 1mM).

Per-cell-type log2 fold change (10mM vs 1mM). * p<0.05, ** p<0.01, *** p<0.001
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Bulk RNA-seq: Tomato nitrate response (10mM vs 1mM). Dashed lines = |log2FC| threshold.


DotPlot: Arabidopsis Col0 on the left, Tomato on the right. Colour scale and dot-size range are harmonised between species.
Arabidopsis (Col0)
Tomato
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scRNA-seq nitrate DE (10mM vs 1mM) for the ortholog pair. At = Arabidopsis Col0; Sl = Tomato.

Arabidopsis–Tomato ortholog mapping.
About this App

Interactive explorer for single-cell RNA-seq data from Arabidopsis thaliana and Solanum lycopersicum roots under low (1mM) and high (10mM) nitrate conditions.

Arabidopsis
  • Genotypes: Col0 (wild-type), nlp7, anac032
  • Seurat object: arab_subpop_6.2.rds
  • Cell type annotation v1.1 (10 types) or v1.3 (13 types with Res/NonRes sub-populations)
  • Proteomics data available for all three genotypes
Tomato
  • Seurat object: int_tom_subpop_6.0.rds
  • Cell type annotation v1.0 (10 types) or v1.1 (12 types with Res/NonRes sub-populations)
Comparison
  • Ortholog lookup via OrthoFinder/KK database
  • DotPlot for cross-species expression comparison
  • Side-by-side scRNA-seq DE results
Inputs and Outputs
  • UMAP: FeaturePlot — gene expression on UMAP embedding
  • DotPlot: % cells expressing (dot size) and mean expression (colour) per cell type; optional split by nitrate condition
  • DE Results: scRNA-seq differential expression (10mM vs 1mM) per cell type using FindMarkers (FM) or DESeq2
  • LFC Heatmap: log2 fold change per cell type with significance annotation
  • Bulk DE: bulk RNA-seq nitrate response results
  • Proteomics: protein abundance (MS2 intensity) per genotype and nitrate condition (Arabidopsis only)

All plots can be downloaded as PDF using the download buttons below each panel.