Full-length target sequences of GeoMx digital spatial profiling probes reveal that gene-promiscuity predicts probe sensitivity to EDTA tissue decalcification

oleh: André Oszwald, Lucia Zisser, Helga Schachner, Christopher Kaltenecker, Gabriel Wasinger, Johannes Rohrbeck, Nicolas Kozakowsky, Andreas Tiefenbacher, Andrew J. Rees, Renate Kain

Format: Article
Diterbitkan: Nature Portfolio 2024-09-01

Deskripsi

Abstract 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.