Cell free RNA Transcript Analysis Script for Equine Asthma at the Molecular Precision Medicine research group, Uppsala University.
In this study, we performed the first characterization of plasma cfRNA in horses and compared circulating cell-free RNA (cfRNA) with partially matched bronchoalveolar lavage (BAL) and whole blood (WB) transcriptomes.
The aims were to:
- Define the cellular and tissue contributions to the cfRNA pool in both healthy horses and EA (external endothelial cells);
- Identify differentially expressed transcripts and pathways;
- Characterize shared and distinct gene signatures of cfRNA with BAL and WB to identify unique cfRNA-derived molecular insights into EA.
This is a public repository containing scripts for the analysis described in the publication:
Circulating cell-free RNA reflects inflammatory and airway remodeling signatures in an equine model of asthma
Birong Zhang, Hanna Agdour, Miia Riihimäki, Sanni Hansen, Amanda Raine
The preprint has posted on bioRxiv.
This work was mainly supported by a grant from The Swedish-Norwegian Foundation for Equine Research, and in part by FORMAS and SciLifeLab.
Raw sequencing data for this project is available at BioProject ID: PRJNA1354409.
The code here primarily performs cell deconvolution analysis, principal component analysis, differentially expressed gene analysis, pathway analysis of cfRNA.
All code is based on R (R version 4.5.0), and the required R packages are listed at the beginning of each code segment. The analysis directories are numbered sequentially according to the main text of the publication. Each script and its corresponding data are located in the same folder.