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

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

in 631/114 / 631/1647/2017 / Decalcification / Edetic acid / Edetic Acid - chemistry / Edetic Acid - pharmacology / Gene expression / Gene Expression Profiling - methods / Humanities and Social Sciences / Humans / Metastasis / multidisciplinary / Probes / Science / Science (multidisciplinary) / Signal to noise ratio / Transcriptome / Transcriptomes / Transcriptomics

2024

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

2024

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

2024

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Journal Article

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

Oszwald, André,

Rees, Andrew J.,

Kaltenecker, Christopher,

Kozakowsky, Nicolas,

Kain, Renate,

Rohrbeck, Johannes,

Tiefenbacher, Andreas,

Wasinger, Gabriel,

Zisser, Lucia,

Schachner, Helga

2024

Overview

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.

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Publisher

Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

Subject

/ Edetic Acid - chemistry

/ Edetic Acid - pharmacology

/ Gene expression