Full-length target sequences of GeoMx digital spatial profiling probes reveal that gene-promiscuity predicts probe sensitivity to EDTA tissue decalcification
GeoMx Digital Spatial Profiling (Nanostring) is a commercial spatial transcriptomics method to selectively analyze regions of interest within intact tissue sections. We show that decalcification with ethylene-diamine-tetra-acetic (EDTA) variably attenuates probe counts, while probes that are more resistant to this effect consequently appear overexpressed after quantile normalization. By determining the undisclosed full-length target sequences of probes used in the human whole transcriptome panel, hereby updating target transcripts and genes, we find that the gene-promiscuity of probes is an important factor that determines sensitivity to EDTA incubation.
Authors
- Gabriel Wasinger (ORCID: https://orcid.org/0000-0002-0323-7180)
- Renate Kain (ORCID: https://orcid.org/0000-0002-2428-543X)
- Christopher C. Kaltenecker (ORCID: https://orcid.org/0000-0002-7795-2726)
- Andreas Tiefenbacher (ORCID: https://orcid.org/0000-0001-7410-6164)
- Lucia Zisser (ORCID: https://orcid.org/0000-0001-9454-2860)
- Helga Schachner (ORCID: https://orcid.org/0000-0002-7116-530X)
- Andrew J. Rees (ORCID: https://orcid.org/0000-0002-6862-6494)
- André Oszwald (ORCID: https://orcid.org/0000-0002-8298-6381)
- Johannes Rohrbeck
- Nicolas Kozakowsky
Institutions
- Medical University of Vienna (AT)
Publication Details
- Journal
- Scientific Reports
- Published
- 2024-09-10
- DOI
- https://doi.org/10.1038/s41598-024-72335-w
- Citations
- 2
- Primary Topic
- Radiomics and Machine Learning in Medical Imaging
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- Universität Wien
- Medizinische Universität Wien