This article introduces Stereo-seq V2, an advanced spatial transcriptomics method designed for high-resolution total RNA mapping on formalin-fixed, paraffin-embedded (FFPE) tissue sections, which are commonly used in clinical settings. This updated technique utilizes random priming to overcome the limitations of traditional methods on degraded FFPE RNA, enabling the capture of non-coding RNAs (ncRNAs) and providing uniform gene body coverage. The source highlights the method's capability to profile host and pathogen transcriptomes simultaneously, as demonstrated in a Mycobacterium tuberculosis (Mtb)-infected mouse model and human samples, and its use in identifying tumor-associated alternative splicing (AS) events in triple-negative breast cancer (TNBC) tissues. Furthermore, Stereo-seq V2 is shown to be effective in elucidating spatial B cell receptor (BCR) clone dynamics, offering potential utility in biomedical research and personalized medicine.
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