Hands-on Bioinformatics Workshop (HBW), Series I

Spatial Transcriptomics Data Analysis

ASOC (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

• Date: Friday, October 04, 2024
• Time: 10:00 - 17:00
• Location: Health Science Centre (HSC) 1504

Workshop Information

The 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.

1. Vignette: GeoMxTools
2. Vignette: SpatialOmicsOverlay
3. Material: Spatial Orgain Atals, Human Brain

Prerequisites

This 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.

1. Bring your laptop
2. Docker
3. R

Materials

Nanostring 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.

1. Human Brain GeoMx DSP data
1. If you can use git, git clone https://github.com/UC-ASOC/HBW1-GeoMxDSP.git
2. Or, download the repo by clicking Code (green button at the top right corner) then Download ZIP from the GitHub repo
2. Human Brain OME.TIFF file
3. Docker App (no need to download)
4. A deck of slides

Objectives

By 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.

1. Nanostring GeoMx DSP Data Analysis
2. Nanostring GeoMx DSP Data Visualization

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.

For more information, please visit Overview on Nanostring.com and Spatial Biology Revealed with the GeoMx DSP by NanoString on YouTube.

FAQ

• How to install Docker?
• How to install R?
• How to download the Workshop materials?
• I am unable to attend the workshop, but I want to analyze the GeoMx data. Is there any way I can do this?
• Can you share a deck of slides and a set of codes?

Registration

• Registration closed
• On a First-come, First-served basis
• Limit to 10 participants for better deliverables during the workshop