Past Workshops
10x Genomics FLEX Sample Prep Workshop
Join our workshop to explore the Chromium Single Cell Gene Expression Flex, a leading-edge technology offering the most sensitive whole transcriptome analysis with unparalleled flexibility. This assay opens doors to profound cellular insights using advanced chemistry suitable for a variety of tissue types, including fresh, PFA-fixed, and FFPE tissues. Learn how to streamline your experiments with scalable workflows that ensure data quality is maintained, even when samples are stored and transported. Discover how sample batching and multiplexing can enhance your research efficiency, significantly reduce variability, and cut per-sample costs by up to 75%. Don’t miss this opportunity to advance your single cell RNA-seq studies and delve deeper into dynamic biological systems.
Spatial Transcriptomic Data Analysis and Software Workshop
This workshop will introduce data analysis workflow with both sequencing and imaging based spatial transcriptomics platforms, using 10x Visium and Xenium as examples. The topics will include an overview of data quality control, preprocessing and visualization, cellular segmentation etc. with 10x proprietary software and state of the art open-source software. A guided tour will be provided on how to run the latest visualization and data exploration tools to support spatial transcriptomics via both the command line and the Jupyterhub of HPC3. Attendees are encouraged to bring their own project data for analysis and discussion.
Introduction Spatial Platform Data Analysis Workflow and Analytical Tools, Jenny Wu, PhD
Interactive Computing On The HPC3 for Spatial Omics, Ivan Chang, PhD
Interactive Computing on the HPC3 for Spatial Omics, Ivan Chang, PhD
Ensembl Browser and REST API Workshops
Sessions presented by Benjamin Moore, PhD, Ensembl Outreach Manager
Single Cell RNA-seq Data Analysis Workshops
Presentations
Intro to Single Cell RNA-seq Data Analysis, Jenny Wu, PhD
(PDF version)
(Video version)Downstream Analysis of Single Cell RNA-seq Data, Jenny Wu, PhD
(PDF version)
(Video version)Tools on HPC3 and 10X Cloud for scRNA-seq Data Primary Processing, Ivan Chang, PhD
(PDF version)
(Video version) Part 1
(Video version) Part 2
DNA Methylation Data Analysis Workshop
Presentations (PDFs)
- Introduction to DNA Methylation Data Analysis, Jenny Wu, PhD
- Using Oxford Nanopore for Long Read Sequencing, Jaz Sakr, GSR
Presentations (Videos)
Hands on Data Analysis Workshop
This workshop served as a summary of the techniques taught in the previous four workshops. Attendees brought their own projects/data/issues
Instruction by Jenny Wu, PhD and Ivan Chang, PhD
Spatial Transcriptomic Data Analysis with an Emphasis on 10x Genomics Visium
Workshop Agenda
Introduction to 10x Visium Spatial Platform Experimental Design and Workflow, Joshua Talboom, PhD
♦ Introduction to 10x Visium – Video Version
♦ Introduction to 10x Visium – PDF version
Visium Data Analysis with 10x Proprietary Software and Open-source Software, Jenny Wu, PhD
♦ Visium Data Analysis – Video Version
♦ Visium Data Analysis – PDF Version
Accessing Analytical Tools on HPC3 for Preprocessing, Ivan Chang, PhD
♦ Accessing Analytical Tool – Video Version
10x Genomics Spatial Workshop Series – Three Sessions
Because cells reside within microenvironments, their functions are influenced by the network cells surrounding them, sending and receiving messages. Spatially resolved biology, including whole transcriptomic and targeted in situ methods, allows scientists to build a more complete view of cellular function in a morphological context, representing a paradigm shift in the study of biological systems. Visium from 10x Genomics is a NGS-based spatial discovery platform that allows whole transcriptome profiling of tissues. The Xenium In Situ platform is an imaging-based solution that provides precise localization of thousands of RNA targets with subcellular resolution, offering true single cell spatial analysis. Insights from these spatial techniques can be combined with single cell data to bring greater resolution and enable a deeper understanding of gene expression patterns, helping researchers develop and refine hypotheses.
January 11, 2024 – Visium
January 18, 2024 – Xenium
January 24, 2024 – Visium Gene Expression
