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

Sci Rep. 2024 Sep 10;14(1):21156. doi: 10.1038/s41598-024-72335-w.

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.

MeSH terms

  • Edetic Acid* / chemistry
  • Edetic Acid* / pharmacology
  • Gene Expression Profiling* / methods
  • Humans
  • Transcriptome

Substances

  • Edetic Acid