Protocol to detect immune levels, abnormal metabolism, and signaling pathways in tumor tissue based on scRNA-seq obtained from patient databases

Abstract

Summary: Malignant tumor cells are typically more active in terms of metabolism and signal transduction compared to immune and normal cells. Here, we present a protocol to evaluate immune levels, abnormal metabolism, and signaling pathways in tumor tissue based on single-cell sequencing based on patient data obtained from the GEO database. We describe steps for tumor immune microenvironment (TIME)-based evaluation, tumor purity assessment, and identification of abnormal signal transduction and metabolic pathways. We then detail procedures for screening hub genes.For complete details on the use and execution of this protocol, please refer to Bai et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Sequence analysis
• Cancer