Most tumours possess a small population of cancer stem cells that divide and differentiate into heterogeneous cancer cells. Investigating cancer stem cell microniches that remain in tumours following neoadjuvant chemotherapy using epitranscriptomics could provide an opportunity to discover novel biomarkers for cancer prognosis and treatment. Conventional spatial transcriptomics techniques require samples from whole tissue sections to be pooled to produce an omics map, which limits analysis to short RNA fragments that can be molecularly barcoded. These short fragments cannot reveal epitranscriptomic features such as alternative splicing variations or the adenosine-to-inosine (A-to-I) editome. However, isolating the region of interest (ROI) can avoid the pooling process and allow for the analysis of full transcripts from rare microniches of interest, revealing epitranscriptomic information.