MOMA single cell core center


MOMA Single-cell Core Center was established in 2022 and is a part of the CellX (The Danish Single Cell Examination Platform) infrastructure.

CellX is hosted by Aarhus University, with strong nodes at University of Southern Denmark and University of Copenhagen, with the aim of giving researchers across Denmark easy access to the necessary cutting-edge technologies and solid downstream data analysis support.

Equipment at MOMA Single-cell Core Center

MOMA Single-cell Core Center features a GeoMx (NanoString), which is a Digital Spatial Profiler (DSP) that provides morphological context in spatial transcriptomics and spatial proteomics experiments from tissue sections, tissue microarrays (TMA), needle biopsies among others.

The GeoMx DSP has the highest plex that covers the entire transcriptome and selected parts of the proteome. It is possible to analyze FFPE-samples, fresh-frozen samples and fixed-frozen samples.

The selection of cells to analyze is based on up to four morphological markers (fluorescently labeled antibodies and/or RNAScope probes). After selection and probe release, the tags are sequenced on Illumina sequencers in-house at the MOMA NGS Core Center.

10X Chromium Controller

MOMA Single-cell Core Center also has a 10X Chromium Controller that performs single-cell barcoding and partitioning through an advanced microfluidics system.

The 10X chromium system can be used for multiple single-cell analysis approaches spanning gene expression, immune-profiling, Multiome ATAC and gene expression and targeted gene expression.

Sara Newell, Jesper Boulund and Kasper Thorsen at Nanostring GeoMx

Digital Spatial Profiling

The principle behind digital spatial profiling with the GeoMx DSP involves the following 6 steps:

(1) Oligonucleotide tags are conjugated to antibodies or RNA probes using aphotocleavable linker. The oligonucleotide tags (with antibodies or RNA probes) are attached to the tissue section through hybridization. The tissue section is then counterstained using morphological markers (antibodies or RNA probes) as well as a nuclear stain.
(2) The GeoMx platform images the tissue using immunofluorescent microscopy so that Regions of Interest (ROI) can be selected. ROIs can be selected in any shape, and with a maximum size of 660 µm x 785 µm. Once ROIs have been selected, these can be divided into cellular compartments called Areas of Illumination (AOI).
(3) UV-light is then used to photocleave the tags which are conjugated to the target proteins/RNAs.
(4) The GeoMx instrument collects the released oligonucleotide tags, and then dispenses these into a 96 well collection plate.
(5) The processes described in (3) and (4) are repeated until all AOIs for all ROIs have been collected.
(6) The collected tags are counted using a nCounter or next generation sequencing, and then mapped to their original target making it possible to localize expression profiles for each ROI/AOI within tissue sections.

The GeoMx DSP workflow. Source: Nanostring

Data Analysis

For GeoMx data, MOMA performs quality control and standard bioinformatic analysis on the GeoMx instrument. Furthermore, MOMA provides a html report with results from an R-workflow based on this work from NanoString.

For 10X analysis, MOMA currently provides quality control only, but can offer advice on open-source pipelines.


The complexity of GeoMx DSP experiments varies greatly from project to project, and we recommend an initial consultation, so that we can assist you with experiment design and planning.

You are welcome to contact us with general enquiries, or to schedule an initial consultation.

Please consult our customer enquiry form in connection with scheduling a consultation, as well as using Nanostring’s GeoMx Morphology Marker Guide to get an idea of which morphology markers may be relevant for your project.

Further Information and Resources

Nature’s Method of the Year: spatially resolved transcriptomics

NanoString’s spatial organ atlas

Best Practices for Spatial Profiling for Breast Cancer Research with theGeoMx® Digital Spatial Profiler

Nanostring publications

Find more information about the CellX platform at biomed.au.dk/cellx or at LinkedIn.


Kasper Thorsen

Manager Single Cell Core Center, PhD, MSc