Laboratory
Head of lab
Csaba Bödör, PhD
Address
H-1085 Budapest, Üllői út 26.
Contact person
Csaba Bödör, PhD bodor.csaba1@med.semmelweis-univ.hu +36-1-215-7300/ext:54462
Facility
Year of commissioning: 2021
Unique features: NanoString’s GeoMx Digital Spatial Profiler (DSP) combines spatial and molecular profiling technologies by generating a whole tissue image at single cell resolution, region-of-interest (ROI) selection using morphology markers and digital expression profiling of ROIs for 10’s-1,000’s of RNA or 10's-100's Protein analytes. This unique combination of high-plex, high-throughput spatial profiling enables researchers to quantitatively investigate the biological implications of the heterogeneity within tissue samples.
Documentation: Array
Quality control: None
Purpose
The NanoString GeoMx® Digital Spatial Profiler system provides the opportunity for researchers to investigate RNA and/or protein expression in situ in connection with tissue morphology at the 1st Department of Pathology and Experimental Cancer Research.
Background
The Molecular Oncohematology Laboratory at the 1st Department of Pathology and Experimental Cancer Research has a long tradition in molecular studies and the institute is well-equipped with cutting edge molecular diagnostic facilities.
The NanoString GeoMx® DSP system offers versatile, established workflows for the spatial characterization of RNA and/or protein expression. The workflow enables researchers to investigate RNA expression in formalin-fixed, paraffin-embedded tissue slides up to the whole-transcriptome level and offers protein expression assays which can be combined to investigate 100’s of protein targets playing a role in immune regulation, tumor microenvironment, etc. The combination of the NanoString GeoMx® DSP system with next-generation sequencing or nCounter readout (both available at the 1st Department of Pathology and Experimental Cancer Research) provides reliable output from all kind of experiments.
Services
NanoString GeoMx® DSP experiment projects with the reagent kits available from the manufacturer.
- NanoString GeoMx® DSP tissue slide preparation and region-of-interest selection for RNA targets
- NanoString GeoMx® DSP tissue slide preparation and region-of-interest selection for protein targets
- Readout with the NanoString nCounter system or next-generation sequencing (Illumina MiSeq or NextSeq2000)
- Downstream data analysis using the on-board software of the GeoMx® DSP system
- Remote Desktop approaches can be used to instrument the GeoMx platform in order to afford ROI selection and data analysis for external researchers.
For further details please refer to the NanoString GeoMx® website or contact us.