Data files

The base condition is C3, i.e. differences are in relation to C3.

Base level is C3, i.e. differences are in relation to C3.

C3 is base condition, i.e. differences are in relation to C3.

C2 is the base condition, i.e. the differences are C1 in relation to C2.

Conda-based DESeq2 pipeline (R 4.5 + Bioconductor) that renders a Quarto report comparing C3 samples to all others in two commands. Bundle includes DET.yml, DET.sh, and DE_C3_vs_all.qmd

This Quarto Markdown file performs differential gene expression analysis using DESeq2, followed by pathway enrichment analysis for Gene Ontology (GO) and KEGG pathways. It includes a heatmap of the top differentially expressed genes and results for GO and KEGG pathway analysis, providing insights into the biological processes affected by experimental conditions.

This ZIP archive contains high-quality PDF figures generated from the postprocessing of xPore RNA modification data. These visualizations summarize key findings and trends across experimental conditions, supporting the interpretation of differential RNA modifications. These figures were produced using a Quarto workflow and are intended for use in reports, presentations, or publications.

This ZIP archive contains the output data generated during the postprocessing of xPore RNA modification analysis. It includes filtered count tables, site-level and gene-level summaries, and other intermediate results used for statistical analysis and visualization.

**Contents may include: **

• • • Site-level counts after filtering
• • • k-mer frequency tables
• • • Gene and transcript-level modification summaries
• • • Data used for generating PCA, volcano plots, and heatmaps

This ZIP archive contains 6 input data tables from the xPore RNA modification analysis, organized by experimental conditions. These tables include modification counts and other relevant data used for downstream analysis and visualization.

This archive contains all necessary files to reproduce the postprocessing and analysis pipeline for [ "omics data analysis in VSMCs"]. The workflow includes a Quarto report, a Conda environment specification (omics-vsmc-env), and input data used for the analysis. The environment ensures reproducibility across systems without requiring hardcoded paths.

Included files:

Postprocessing_no_cov_filter.qmd — The main Quarto report for data visualization and results.

renv.lock and renv/ — R environment ...

This Quarto Markdown file contains a step-by-step workflow for analyzing xPore RNA modification data. It includes filtering, statistical analysis, and visualization to identify and explore differences in RNA modifications between samples. The outputs include:

• PCA plots to check sample clustering
• k-mer counts to see sequence patterns
• Volcano plots to show significant changes
• Heatmaps of modification levels
• Other visual summaries to help interpret the results

This workflow makes it easy ...

This report is the result of running a Quarto Markdown file designed for visualizing and analyzing xPore RNA modification data. It provides clear insights into RNA modifications across different experimental conditions, serving as both a visual and analytical reference for the study.

**Key sections include: **

• PCA plots before and after filtering
• Counts of k-mers at different filtering thresholds
• Gene- and transcript-level modification summaries
• Volcano plots for differential modification ...

This file contains the processed LC–MS/MS results for intracellular metabolite quantification using the isotope-ratio approach. It provides the C12/C13 ratios for all metabolites in each sample, calculated relative to the 13C-labelled internal standard. The dataset also includes the retention times and the measurement quality scores for each metabolite, enabling assessment of peak identification and data reliability. The raw LC–MS/MS data used to generate these results are available from the ...

This file contains the data generated for extracellular metabolite quantification using HPLC–MS. It includes the extracted ion chromatograms (EICs) and total ion chromatograms (TICs) for all measured metabolites within the samples and within the calibration standards, as well as the peak heights obtained for both the calibration standards and the extracellular samples. These data support the calculation of metabolite concentrations based on calibration curves.

This file contains metadata associated with the metabolomics sampling procedure. It includes (i) optical density (OD) measurements of each culture at the time of sampling for intracellular and extracellular metabolite quantification, and (ii) the sample label table used for intracellular metabolite analysis. The table provides, for each sample, the sample label/number, collected sample volume, quenching volume, and the mapping to the corresponding biological sample.

This file contains the data generated for glycogen quantification. It includes the raw absorbance measurements at 540 nm for each sample, the corresponding culture optical densities (OD) at the time of sampling, and the calibration curve data (absorbance values and associated glucose standards) used to calculate glucose concentrations from the measured absorbance values.

Biochemical Reaction Networks Biochemical Reaction Networks transform static protein-protein interactions (PPI) network into dynamic, mechanistic models by decomposing each interaction into underlying molecular events like phosphorylation and complex formation. Using SPADAN toolbox (DOI:10.1093/bioinformatics/btad079), we expands PPI network into biochemical reactions network.

Ordinary Differential Equation Model Equations Kinetic descriptions of biochemical reactions related to each renal cell ...

Data submited to Plant Physiology

Immunoblotting gel images, annotations, results