Differential gene expression and pathway enrichment using Deseq2
SEEK ID: https://fairdomhub.org/assays/2573
Modelling analysis
Projects: OMICS of vascular smooth muscle cells under oxidative stress
Investigation: ONT direct RNA Sequencing
Study: Differential transcript expression analysis
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Creators and SubmitterViews: 5
Created: 12th Feb 2025 at 11:37
Last updated: 19th Dec 2025 at 13:01
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Projects: Group Data Science, Methylation differences during respiratory infection, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, OMICS of vascular smooth muscle cells under oxidative stress, Systems genetics of lung health and asthma (GWAS, PGS, QTL)
Institutions: Forschungszentrum Borstel
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 ...
Projects: Group Data Science, Group Microbial Interface Biology, Core Facility Fluorescence Cytometry, Targeting the immunoproteasome: Analyzing the biological effects of specific versus pan inhibition, Macrophage and neutrophil redox proteome in infection with Mycobacterium tuberculosis, Methylation differences during respiratory infection, Lipid droplet formation and dynamics in murine macrophages, OMICS of vascular smooth muscle cells under oxidative stress, Systems genetics of lung health and asthma (GWAS, PGS, QTL), Archaean stimulation of human primary PBMCs and PBMCs monocytes
Web page: https://fz-borstel.de
Programme: Research Center Borstel
Public web page: Not specified
Submitter: Ayat Ismail
Investigation: ONT direct RNA Sequencing
Assays: Differential gene expression and pathway enrichment using Deseq2
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.
