ProbeST: a custom probe design pipeline for dual host–pathogen Spatial Transcriptomics
Sofia Rouot, Ireen van Dolderen, Patrick Rosendahl Andreassen, Solène Frapard, Sybil A. Herrera-Foessel, Hailey Sounart, Sami Saarenpää, Julia A. Vorholt, Stefania Giacomello · 2026
Read ProbeST: a custom probe design pipeline for dual host–pathogen Spatial Transcriptomics by Sofia Rouot, Ireen van Dolderen, Patrick Rosendahl Andreassen, Solène Frapard, Sybil A. Herrera-Foessel, Hailey Sounart, Sami Saarenpää, Julia A. Vorholt, Stefania Giacomello (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/PMC13295851.txt.
Description
Sofia Rouot and co-authors introduce ProbeST in 2026, free software for designing probes that map gene activity in tissue slices. Commercial probe sets cover only humans and mice, which blocks studies of infection where both host and germ matter.
The team tested their pipeline on preserved mouse gut cells infected with Salmonella, pairing custom germ probes with a standard mouse panel. Both host and bacterial signals were picked up cleanly in place, and host response genes sat near bacterial ones. The authors argue the workflow opens spatial mapping to non-model species and host-pathogen work.
Catalog record
| CREATOR | Sofia Rouot, Ireen van Dolderen, Patrick Rosendahl Andreassen, Solène Frapard, Sybil A. Herrera-Foessel, Hailey Sounart, Sami Saarenpää, Julia A. Vorholt, Stefania Giacomello |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 48338 |
| LICENSE | https://creativecommons.org/licenses/by/4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |