Single-cell RNA sequencing (scRNA-seq) offers a wide array of applications across diverse biological models, including both murine and human systems, each presenting unique experimental challenges and potential exciting discoveries. This presentation will examine two distinct scRNA-seq applications, comparing human and mouse model systems. It will discuss the inherent complexities and potential difficulties that may arise at key stages of the experimental protocol. Furthermore, it will emphasise the importance of pilot studies in mitigating batch effects and optimizing experimental workflows. The presentation will acknowledge that suboptimal cellular conditions may necessitate suboptimal methodological choices, which can pose challenges for downstream analysis. Proactive approaches, which consider the capabilities and limitations of bioinformatic correction, are essential for ensuring data integrity and achieving cost-effective research outcomes.