Intro to NanoString

GeoMx® DSP stands at the powerful intersection of tissue imaging technology and genomic sciences.  It enables investigators to finely dissect the fundamental features of any tissue and ask critical questions concerning tissue organization, cellular interactions, and disease pathology.  

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Tools & Technologies

GeoMx developer platform - Get started with the NanoString platform  

See what other analysis methods have been developed for GeoMx DSP data


For this hackathon participants will have access to a kidney dataset profiling specific regions to better understand the changes that occur during kidney disease development.  This dataset consists of three normal tissue samples and four samples with diabetic kidney disease.  High resolution slide images and corresponding spatially resolved gene expression data for selected regions of interest (ROIs) on the slides will be available. 

Gene expression within each ROI was profiled using the Human Whole Transcriptome Atlas (WTA) from NanoString which captures expression from 18,000+ human protein-coding genes on the GeoMx DSP by tagging unique gene sequences physically within the tissue and then releasing specifically within the ROI areas.

Start with the README and then download the fully annotated dataset HERE


Diabetic kidney disease is a type of kidney disease caused by diabetes.  Diabetes is the leading cause of kidney disease. About 1 out of 3 adults with diabetes has kidney disease. 

Scientists are trying to better understand the changes that occur during kidney disease development.  GeoMx DSP enables a unique way for scientists to analyze these changes by providing gene expression in spatial context.  Each study generates large amounts of data associated with multiple images creating challenges for scientists to interpret and derive biological conclusions.

As an example, we can use PCA to visualize the separation in anatomical structures such as tubules vs glomeruli:

An example of using spatial information in conjunction with gene expression results:

See what else people have used the GeoMx data with previously:


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