Digital Spatial Profiling Service (Nanostring GeoMx Cancer Transcriptome Atlas)

Description

Cellecta’s Digital Spatial Profiling (DSP) Service for cancer research focuses specifically on RNA profiling using the NanoString GeoMx Cancer Transcriptome Atlas Probe set, which targets ~1,800 human genes in 55 pathways critical to immune response, tumor biology and microenvironment. The technology enables the measurement of patterns of gene expression in specific targeted areas of interest on tumor sections

Applications of RNA Spatial Profiling in Cancer Research:
• Identifying genes associated with tumor infiltration
• Characterizing markers of the immune response
• Profiling normal and diseased tissues in the same sample
• Monitoring therapeutic response, and more.
FFPE tissue sections provided by you will be stained with the following:

– An APC- or PE- fluorescently labeled antibody detecting a morphology marker enabling you to identify cell types of interest in the sample
– A panel of pre-mixed biological probes targeting oncology relevant RNA transcripts and incorporating an UV-cleavable DNA barcode

Using the fluorescent morphology marker for guidance, defined regions of interest (ROIs) are illuminated with UV light to cleave barcoded labels from the RNA probes. The probes from each ROI are then collected in separate wells and quantified using NGS. The resulting read number of each probe then correlates to the expression level of its gene target.
A typical workflow is completed with a document that reports the study design, procedures used, and the results obtained. Reports will be customized for the investigator’s needs but will generally include both text and digital files that cover:
• Summary of the objectives, goals, and results as discussed at the start and end of the project
• Images (and high-resolution image files) corresponding to the stained slides and ROIs of interest
• Data analysis elements including QC, normalization methods, expression count tables (also provided as files), differential gene expression and pathway analysis with statistical tests as appropriate and guided by the investigator

The shown price is valid for the digital spatial expression profiling of up to 12 ROIs on 1 slide which may feature multiple sections, and includes the optimization of the fluorescently labeled antibody for the GeoMx instrument using test tissue section slides provided by you. In case you are interested in the analysis of more than 12 ROIs and/or more than 1 slide, please contact us for a quotation.