Scripts to analyze innate T cell transcriptomes from Gutierrez-Arcelus et al., Nature Communications, 2019 (doi.org/10.1038/s41467-019-08604-4).
In the low_input_rnaseq folder, you'll find a script to re-create the PCA that revealed the innateness gradient on PC1 (Fig. 2a-b).
In the single_cell_rnaseq folder, you'll find a script to re-create the PCA and UMAP of our single-cell RNA-seq data (Fig. 8b, Supplementary Fig. 15a)
Input files are available as Supplement Files in GEO with accession number GSE124731.