RNA-seq identifies markers of high altitude exercise adaptation

This repository describes the analysis of whole blood RNA-seq of elite skaters before and after intense exercise, with high altitude adaptation.

Seven elite female speed skaters spent 18 days in live-high, train-high (LHTH) setting. After 18 days, whole blood samples were collected before and after an intense bout of exercise. Samples were globin-depleted and sequenced using poly-A selected, strand-specific RNA-seq.

Publications

Preprint

Andrey S. Glotov, Irina E. Zelenkova, Elena S. Vashukova, Anna R. Shuvalova, Alexandra D. Zolotareva, Dmitrii E. Polev, Yury A. Barbitoff, Oleg S. Glotov, Andrey M. Sarana, Sergey G. Scherbak, Mariya A. Rozina, Victoria L. Gogotova, Alexander V. Predeus, RNA sequencing of whole blood defines the signature of high intensity exercise at altitude in elite speed skaters, 2021.

Data

Expression tables generated by STAR + rsem pipeline, as well as some annotation files necessary to reproduce the analysis. Place all the files into your working directory and unpack them. Raw RNA-seq reads were deposited in GEO database as GSE164890.

Analysis

• functions.R contain all necessary R functions that need to be sourced before performing other analysis;
• all_analysis_and_figures.R contains all the analysis and data visualization code:
  • differential expression, batch correction, and PCA analysis of the bulk RNA-seq data;
  • pathway enrichment with fGSEA and clusterProfiler;
  • putting our dataset in context of previously published microarray datasets (8 experiments);
  • generating exclusive markers for all major cell types present in whole blood;
  • identification of cell type populations from the bulk RNA-seq;
  • annotation and plotting of key genes up- and down-regulated after exercise at high elevation;
  • correlation plot for peer review.

Single cell RNA-seq datasets that were used to generate the cell type signatures for most cell types present in whole blood are GSE149938 and 10x Genomics PBMC 10k.

Figures

All manuscipt figures can be reproduced using the R scripts in this repository.

Contacts

Please contact Alexander Predeus (predeus at bioinf me) or Andrey Glotov (anglotov at mail ru) with all questions and requests.