Combining BRD4 inhibition with SMAC mimetics: Single-cell CITE-seq analysis

This is a code repository for the paper Slavic Obradovic et al. "Combining BRD4 inhibition with SMAC mimetics restricts tumor growth and triggers immune surveillance in preclinical cancer models" in Cell Reports Medicine.

This repository covers the analysis of CITE-seq data.

The data is available in GEO under accession number GSE269602

Experiment

Investigation of the effect of SMACm and BETi on the tumor microenvironment. Three PAN02 mice per treatment group, four treatment groups in total: Natrosol, SMAC mimetic (SMACm), BET inhibitor (BETi), and SMACm + BETi combination.

Processing

• SevenBridges Upload
• Sequencing metrics
• Prepare SingleCellExperiment

Notebooks and figures for the paper

• Initial processing with Seurat
• Figure exports
• Analysis of protein expression