The Expression & Spatial Profiling (ESP) Core Facility, formerly known as nCounter Core Facility, was established in 2011 and rebranded in 2026. The ESP Core Facility is part of the CellNetworks Core Technology Platform at Heidelberg University and the MULTI-SPACE platform of the Health & Life Science Alliance. The facility offers state-of-the-art methods for multiplex mRNA and miRNA expression profiling (Bruker nCounter SPRINT Profiler), as well as Digital Spatial Profiling at the transcript level (Bruker GeoMx Digital Spatial Profiler) and protein level (Bruker GeoMx Digital Spatial Profiler, Lunaphore COMET). In addition, the facility provides various analytical methods for quality control of RNA and DNA samples. 

In the DFG’s research infrastructure portal RIsources, the Expression & Spatial Profiling Core Facility is listed under RI_00563 (nCounter SPRINT Profiler, GeoMX Digital Spatial Profiler) and RI_00613 (Lunaphore COMET platform).

The nCounter SPRINT Profiler (Bruker) is suitable for multiplexed expression profiling of around 800 mRNAs or miRNAs. Maximum flexibility is ensured through the use of both pre‑defined panels and fully customizable gene sets. Supported sample types are total RNA, cell lysates, FFPE (formalin-fixed, paraffin-embedded)-derived RNA and PAXgene-lysed whole blood. Only very small amounts of RNA (25-150ng, depending on the chosen gene set) are required for the analysis. Reverse transcription of the RNA is not required. 

For multiplex analysis, the device uses fluorescently labelled reporter probes, which are highly resistant to poor RNA quality due to their length of approx. 100 bases and are therefore ideal for samples that are difficult to analyze, such as FFPE samples. The application of a unique coding technology enables the direct counting of single RNA molecules at all levels of biological expression, with a sensitivity and specificity comparable to Real Time PCR (RT PCR). 

The nCounter SPRINT Profiler is a perfect system for the validation of RNAseq data, the targeted analysis of signaling pathways, the expression profiling of defined gene lists (individual or predefined) as well as for the validation of biomarkers. The ESP Core Facility offers a full service for nCounter SPRINT Profiler-based analyses.

High‑throughput, spatially resolved multiplex RNA and protein profiling provides deep molecular insights. It enables compartment‑specific analysis and is especially valuable when sample material is limited, allowing comprehensive profiling from a single tissue section.

The GeoMx Digital Spatial Profiler (DSP, Bruker) builds on these advantages by offering a highly flexible and non‑destructive platform for spatial biology. Designed to integrate seamlessly with standard histology workflows, it supports both FFPE and fresh‑frozen samples. Researchers can perform RNA and protein profiling separately or combine them into a multi‑omics approach, depending on the needs of their study. 

The GeoMx DSP platform combines whole‑slide imaging with high‑plex digital profiling to deliver spatially resolved data across hundreds to thousands of analytes per experiment (RNA: up to 18,000 plex, protein: up to 1,200 plex). Assay content can be customized, supporting up to 400 RNA and up to 40 protein targets. Depending on the chosen assay, RNA and protein levels can be quantified using either the nCounter SPRINT profiler or next‑generation sequencing (NGS).

Its digital barcoding technology provides highly quantitative data across a wide dynamic range, making it possible to detect subtle expression differences even in heterogeneous microenvironments. No special glass slides are needed. The system offers a large scanning area with flexible region-of-interest (ROI) and area-of-interest (AOI) selection. This morphology‑guided region selection ensures that rare cell populations and biologically relevant niches are captured accurately, improving the precision of spatial analyses in oncology, immunology, neuroscience, and infectious disease research. 

With its scalability, high plex, and preserved tissue context, the GeoMx DSP platform offers a powerful solution for biomarker discovery, pathway analysis, for complementing histology and bulk sequencing with essential spatial information across diverse disease models as well as comprehensive tissue characterization across diverse disease models. It can easily be combined with the COMET (Lunaphore), the PhenoCycler-Fusion (Akoya) and other platforms. The ESP Core Facility provides full service for GeoMx DSP-based analyses, excluding data analysis.

The COMET platform (Lunaphore) enables the simultaneous visualization of up to 40 antibodies on one to four tissue samples. The automated workflow and a precise microfluidics system ensure high reproducibility. In addition to proteins, specific RNA samples can also be stained.

The tissue samples (FFPE or Fresh Frozen) are directly or indirectly stained and imaged. The background is automatically subtracted. The generated images are saved in tiff format and can therefore be analyzed with common programs.

Workflow COMET platform:

After registering with iLabs and requesting a "Lunaphore COMET Consultation request" in iLabs, the project and the experiments are discussed. After completing the "Lunaphore COMET sample run" request in iLabs and sending all required materials and samples, test runs are carried out first and then the experiments themselves after further discussion. The data can then be collected or downloaded as agreed.

For dedicated quality control analyses, we use the Agilent TapeStation and the Qubit system from Thermo Fisher Scientific.