Hands-on Bioinformatics Workshop (HBW), Series 1Spatial Transcriptomics Data AnalysisASOC (Applied Spatial Omics Centre) is hosting a Spatial Transcriptomics Data Analysis Workshop focusing on Nanostring GeoMx DSP data analysis and visualization to profile the whole transcriptome at the University of Calgary. Venue
Workshop InformationThe workshop will include lectures and hands-on tutorials to cover data (pre)processing, normalization, and visualization of the Nanostring GeoMx DSP data. Nanostring offers a set of R packages that enables comprehensive QC/analysis of the GeoMx DSP data and the following two vignettes will be covered in the Workshop. In addition, Nanostring generously provided the Spatial Organ Atlas and the Human Brain dataset will be used to generate results. The goal is to provide comprehensive analysis schemes for Spatial Transcriptomics data analysis, specifically Nanostring GeoMx DSP data, and other bioinformatic tasks.
PrerequisitesThis workshop is for beginners and no prior knowledge of Linux/Docker/R is required. Basic Linux commands will not be covered, however, you'll type in a couple of lines of Linux commands to deploy a Docker app. The Instructor will use a MacBook throughout the Sessions and it would be easier to follow if participants brought a MacOS- or Linux-based machine. A Windows machine would still be okay and please make sure to have Docker and R installed on your machine. MaterialsNanostring generously agrees that ASOC can directly distribute and host a subset of Human Brain GeoMx DSP data for this Workshop and participants should download the following two items before the workshop on their machine.
ObjectivesBy the end of this workshop, participants will be able to understand the GeoMx DSP data structure, generate diagnostic plots for QC, carry out statistical testing between user-defined groups, and visualize the segments on a tissue image. Participants can preview a set of codes and outputs below. Workshop Schedule
About Nanostring GeoMx Digital Spatial Profiler (DSP)GeoMx DSP is the most flexible and robust spatial multi-omic platform for the analysis of formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue sections. GeoMx is the only spatial biology platform that non-destructively profiles the expression of RNA and protein from distinct tissue compartments and cell populations with an automated and scalable workflow that integrates with standard histology staining. It uses fluorescent imaging reagents to visualize tissue and oligo-tagged reagents for expression analysis. After selecting regions of interest (ROI), DNA oligos are released, and collected in a 96-well plate. Expression levels are readout using Next-Generation Sequencing (NGS) or nCounter and analyzed using the DSP interactive software. FAQ |
 How to Register
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Hands-on Bioinformatics Workshop (HBW), Series 1Spatial Transcriptomics Data AnalysisASOC (Applied Spatial Omics Centre) is hosting a Spatial Transcriptomics Data Analysis Workshop focusing on Nanostring GeoMx DSP data analysis and visualization to profile the whole transcriptome at the University of Calgary. Venue
Workshop InformationThe workshop will include lectures and hands-on tutorials to cover data (pre)processing, normalization, and visualization of the Nanostring GeoMx DSP data. Nanostring offers a set of R packages that enables comprehensive QC/analysis of the GeoMx DSP data and the following two vignettes will be covered in the Workshop. In addition, Nanostring generously provided the Spatial Organ Atlas and the Human Brain dataset will be used to generate results. The goal is to provide comprehensive analysis schemes for Spatial Transcriptomics data analysis, specifically Nanostring GeoMx DSP data, and other bioinformatic tasks.
PrerequisitesThis workshop is for beginners and no prior knowledge of Linux/Docker/R is required. Basic Linux commands will not be covered, however, you'll type in a couple of lines of Linux commands to deploy a Docker app. The Instructor will use a MacBook throughout the Sessions and it would be easier to follow if participants brought a MacOS- or Linux-based machine. A Windows machine would still be okay and please make sure to have Docker and R installed on your machine. MaterialsNanostring generously agrees that ASOC can directly distribute and host a subset of Human Brain GeoMx DSP data for this Workshop and participants should download the following two items before the workshop on their machine.
ObjectivesBy the end of this workshop, participants will be able to understand the GeoMx DSP data structure, generate diagnostic plots for QC, carry out statistical testing between user-defined groups, and visualize the segments on a tissue image. Participants can preview a set of codes and outputs below. Workshop Schedule
About Nanostring GeoMx Digital Spatial Profiler (DSP)GeoMx DSP is the most flexible and robust spatial multi-omic platform for the analysis of formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue sections. GeoMx is the only spatial biology platform that non-destructively profiles the expression of RNA and protein from distinct tissue compartments and cell populations with an automated and scalable workflow that integrates with standard histology staining. It uses fluorescent imaging reagents to visualize tissue and oligo-tagged reagents for expression analysis. After selecting regions of interest (ROI), DNA oligos are released, and collected in a 96-well plate. Expression levels are readout using Next-Generation Sequencing (NGS) or nCounter and analyzed using the DSP interactive software. FAQ |
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How to Register
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