/ajrcmb_marijuana_rnaseq

Analysis code accompanying "Chronic marijuana use is associated with gene expression in bronchoalveolar lavage" (ATS Journals)

Primary LanguageR

"Chronic Marijuana Use Is Associated with Gene Expression Changes in BAL"

Summary: We found differences in bronchoalveolar lavage (BAL) gene expression profiles from long-term, frequent marijuana smokers without concurrent tobacco use compared to those of tobacco-only smokers and of non-smokers, including differentially expressed genes and pathways suggestive of altered respiratory immunity.

  • This research letter is open access at ATS Journals.
  • Deidentified participant metadata and raw RNA-seq data are publicly available at GEO, accession GSE155213.

File Structure

├─ Data
│   └─ count_table.txt             # RNA-seq counts (gene x sample)
│   └─ participant_metadata.txt    # (sample x variable)
├─ Scripts                         # 22 scripts; data processing & analysis
└─ Results                         
│   └─ ResultsTable1.xlsx          # pairwise diff. expression results (multiple tabs) 
│   └─ ResultsTable2.xlsx          # GO enrichment results (multiple tabs)

Links

Citation

Liu C, Gaydos J, Johnson-Paben R, Kechris K, Burnham EL, Sharma S. Chronic Marijuana Use Is Associated with Gene Expression Changes in BAL. American Journal of Respiratory Cell and Molecular Biology. 2022 Feb;66(2):238-9.