Spatial transcriptomics
GeoMx DSP data analysis
Deep RNA or protein profiles of the tissue regions and compartments that matter, with statistics that hold up.
What GeoMx DSP measures
GeoMx profiles RNA or protein from regions of interest chosen on a tissue section using immunofluorescence morphology markers. Within each region, compartments such as tumour and stroma can be separated with masks and profiled independently, up to the whole transcriptome. Rather than single cells, GeoMx gives deep, quantitative profiles of tissue compartments, which suits biomarker and comparative studies.
Strengths
- Whole-transcriptome or high-plex protein profiling from defined tissue regions
- Compartment-specific profiles, for example tumour versus immune versus stroma
- Works well with FFPE archives and clinical cohorts
- Region selection guided by pathology and morphology markers
How we can help with GeoMx DSP data
ROI strategy
Planning region and compartment selection so comparisons are balanced and interpretable.
QC and normalization
Segment and probe QC, limit-of-quantitation filtering and normalization suited to your design.
Differential expression
Mixed-effects models that respect patients, slides and regions as levels of replication.
Deconvolution
Estimating the cell type composition of each region from reference profiles.
Pathway analysis
Gene set and pathway analysis to interpret compartment-specific changes.
Figures
Region-level plots, heatmaps and image overlays for publication.
Related technologies
Working with GeoMx DSP data?
Tell us about your samples, panel and question. The first consultation is free.