From molecules to data: a primer on RNA sequencing methods and artifact generation

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RNA sequencing is a foundational tool for quantifying gene expression across diverse biological contexts. However, the intricate and diverse processes of converting RNA into a sequenceable cDNA library introduce molecular artifacts and systemic biases. In this primer, I will walk through the steps of bulk, single-cell, and spatial RNA sequencing and describe how common artifacts are generated, including internal oligo(dT) priming, PCR mispriming, and TSO-TSO artifacts. I will also describe the pervasive impact of poor sample quality. This primer will provide an introduction to the molecular processes of RNA capture, how artifacts are generated, and how they impact transcriptomic analysis.

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