Show Notes
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 the transcript's portrayal of FFPE RNA handling, random-priming total RNA capture, uniform gene-body coverage, subcellular spatial resolution, DV200 tolerance, gene detection advantages, non-coding RNA profiling, TNBC CNAs (ESR1), GIPC1 alternative splicing, MTB host-pathogen mapping, and BCR repertoire analysi
- transcript topics: FFPE RNA degradation and formaldehyde cross-linking; Random-priming with 6N primers versus poly-A capture; Uniform gene-body coverage and 3' bias elimination; DNA nano-ball (DNB) arrays at 500 nm spacing for subcellular spatial resolution; Total RNA and non-coding RNA profiling; DV200 metrics and nine-year-old FFPE sample tolerance
QC Summary:
- factual score: 10/10
- metadata score: 3/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 1
- metadata issues found: 3
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 in GIPC1 (exon skipping)
Internal QC note: metadata cleanup is still recommended before publication.
QC result: Warning. Review the flagged items before publication.
