OMICS of vascular smooth muscle cells under oxidative stress

The FZB is the lung research center of the Leibniz Association and is therefore committed to the motto “theoria cum praxi”.

The FZB sees its scientific and socio-political task in basic, disease- and patient-oriented lung research and training in this field. The field of research includes chronic inflammatory diseases of the lung of infectious and non-infectious environmental and behavioral origin. Research focuses on tuberculosis, infections with non-tuberculous mycobacteria and other bacterial ...

Human aortic smooth muscel cells (Thermo Fisher Scientific, C-007-5C, LOT: 2164581) were treated with TGB1 or PDGF/L1B to induce the contractile or synthetic SMC phenotype. As part of a multi-omics analysis, we conducted mass spectrometry to quantify protein levels of cell lysates using a HPLC-ESI-MS/MS system (HPLC=high pressure liquid chromatography, Ultimate 3000 UPLC system; ESI=electrospray ionization) and an Orbitrap Exploris™ 480 mass spectrometer. MS data were analyzed and normalized with ...

Majority direction kmer data files were used for the analysis. e.g: results/analysed_icg/xpore_cdna.all/diffmod_s1-s2/majority_direction_kmer_diffmod.table. which has been renamed to : s1_s2.table as uploaded here.

Cell line: Human aortic smooth muscel cells (Thermo Fisher Scientific, C-007-5C, LOT: 2164581)

Technical replicates: n=4 per condition

Conditions: C3 = TGFB1-treated SMCs C4 = PDGF-BB/IL1B-treated SMCs

Cell line: Human aortic smooth muscel cells (Thermo Fisher Scientific, C-007-5C, LOT: 2164581)

Technical replicates: n=4 per condition

Conditions: C3 = TGFB1-treated SMCs C4 = PDGF-BB/IL1B-treated SMCs

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 ...

Specifications and workflow of MS proteomics