Base by Base19 Nov 2025

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)

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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, and applications
- 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.

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