Past Workshops
Experimental Design Sessions with10x-perts
The vast complexities of biology require approaches to build a complete picture, starting from single cells to tissues and beyond. At 10x Genomics, we provide single cell, spatial, and in situ technologies that fuel scientific discoveries and drive exponential progress. Unravel highly complex biological systems, while bringing into focus the details that matter most.
Join us to learn how Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from10x Genomics can help you push the boundaries of your research. Uncover molecular insights, dissect cell-type differences, investigate the adaptive immune system, detect novel subtypes and biomarkers, and map the epigenetic landscape cell by cell. Enabling deeper insight into cancer, immunology, neuroscience, and developmental biology, 10x Genomics gives researchers the ability to see biology in new ways.
Please email Christine Kao to schedule your appointment-christine.kao@10xgenomics.com
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
