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Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue
Published on: April 27, 2012
Full-length target sequences of GeoMx digital spatial profiling probes reveal that gene-promiscuity predicts probe
André Oszwald1, Lucia Zisser2, Helga Schachner1
1Department of Pathology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
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.

