This repository contains the code and some results associated with the B7H3 CAR T + CXCR2 bulk RNAseq experiment.
Breifly, two types of CAR T cells were created:
- B7H3 CAR T cells
- B7H3 CAR T cells + CXCR2 ("BC2") - same CAR protein, but an extra protein (CXCR2) included in the plasmid
These two CAR T cells were submitted to three conditions:
- No stimulation
- B7H3 bead stimulation
- IL-8 cytokine stimulation (a ligand for CXCR2)
The cells were then collected for bulk RNAseq to compare the CAR T cells against each other for each stimulation.
The main repository contains R markdown files detailing the analysis of the mapped reads. Mainly done by subsetting the stimulation conditions, running DESeq2, and then GeneTonic exploration of the resulting pathway enrichment analyses.
Files folders in the repository contain:
The bash files used to run FastQC and STAR mapping on the cluster server
CSV files containing the pathway enrichment results when comparing BC2 vs B7H3 CAR T cells for a given stimulation. Rdata files containing the DESeq object, results object, GeneTonic topgo object, and annotation object. Everything needed to run the GeneTonic browser function
Initial plots generated after DESeq2 results were put into GeneTonic.
Gene list csv files detailing the results of the DESeq2 comparisons.
Plots that were a result of 2023_10_09_final_figures.Rmd and 2023_10_23_plot_adjustments.Rmd There were many iterations of these files, as many small tweaks were made to make plots for publication. So not all plots may have their original code in the markdown files. See subfolders for more recent plots that are reflected in the code.