202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues

Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues Music:Enjoy the music based on this article at the end of the episode. License:CC BY 4.0 International License (CC BY 4.0) Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/stereo-seq-v2-spatial-total-rna-mapping-in-ffpe-tissues ️ Episode:202: Stereo-seq V2: Spatial Total RNA Mapping in FFPE Tissues ️ Season:1 Article title:Stereo-Seq V2: Spatial Total RNA Mapping in FFPE Tissues Journal:Cell DOI:10.1016/j.cell.2025.08.008 QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-11-19. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited transcript sections describing FFPE RNA degradation and cross-linking, random-priming with 6N primers, uniform gene-body coverage and 3' bias elimination, 500 nm DNA nano-ball (DNB) arrays for subcellular spatial resolution, total RNA mapping including non-polyadenylated RNAs, DV200 tolerance, large-gene detect- transcript topics: FFPE RNA degradation and formaldehyde cross-linking; Random-priming with 6N primers vs poly-A capture; Uniform gene-body coverage and 3' bias elimination; DNA nano-ball (DNB) arrays at 500 nm spacing for subcellular resolution; Total RNA mapping including non-polyadenylated RNAs; DV200 tolerance in aged FFPE samples QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- Stereo-Seq V2 uses random primers (6N) to capture total RNA from FFPE tissues- Random priming yields uniform coverage across the entire gene body and removes 3' bias- Total RNA mapping includes non-polyadenylated RNAs enabling non-coding RNA profiling- DV200 tolerance: low as 18% in nine-year-old FFPE samples- Gene detection exceeds poly-A based methods with >23,000 genes missed by poly-A techniques- Alternative splicing events identified (e.g., GIPC1 exon skipping) QC result: Pass.