Workshops

In this Bioinformatics Bootcamp, you will embark on the Visium HD Spatial Gene Expression data analysis journey with us. Running your Visium HD assay is just the beginning. Next comes the exciting work of data analysis, enabled by seamless exploration from whole tissues down to single transcripts, leading to novel biological insights.

In our first session, we will begin with a guided tour of the 10x Cloud Analysis platform, and start our journey by processing raw data from a human colon cancer sample with Space Ranger using the 10x Cloud. Next, we will assess data quality using the web summary and then dive into Loupe Browser for manual image alignment, in-depth data exploration, and cell-type mapping. We’ll then take these insights to community-developed tools, allowing for further exploration of the tumor’s spatial organization and cellular interactions.

In this learning series, you will:

• Gain hands-on experience with the 10x Cloud Analysis platform, learning to create projects, upload files, run analyses, and download results efficiently.
• Explore and assess data quality using the Space Ranger web summary, followed by in-depth data exploration and cell-type mapping with Loupe Browser.
• Utilize community-developed tools to further investigate the tumor ecosystem, enhancing your understanding of spatial gene expression data.

By the end of the learning series, participants will acquire a foundational understanding of analyzing Visium HD data.

Each webinar in this series will consist of a ~40 minute presentation followed by a live Q&A session.

Session 1: Introduction to Visium HD data analysis with 10x Cloud

February 10, 2025 | 10:00 AM – 11:00 AM PT

Samantha Shelton, PhD

Science & Technology Advisor
10x Genomics

• Introduction to Visium data analysis
• Overview of Space Ranger for whole transcriptome spatial expression analysis
• Understand key steps in Space Ranger pipelines
• Overview of key output files generated by the pipelines
• Understand the quality metrics and know what to look for to quickly gauge the quality of the data

Session 2: Hands-on Visium HD data visualization

February 12, 2025 | 10:00 AM – 11:00 AM PT

Daphne Cooper, PhD

Sr. Science & Technology Advisor
10x Genomics

Josh Talboom, PhD

Science & Technology Advisor
10x Genomics

• Loupe Browser data visualization demonstration
• Hands-on experience interacting with data from the Visium HD Gene Expression solution
• Exercises will include exploring your results with Loupe Browser

This workshop will introduce data analysis workflow with both sequencing- and imaging-based spatial transcriptomics platforms, using 10x Genomics Visium and Xenium as examples. The topics will include an overview of preprocessing and data visualization with both 10x Genomics proprietary software and the state-of-the-art open-source software. New topics such as Visium HD and Xenium 5k data analysis will be discussed including cellular niche and spatial differential analysis methods. A guided tour will be provided on how to run the latest visualization and data exploration tools to support spatial transcriptomics via command line and Jupyter Hub on HPC3. Attendees are encouraged to bring their own project data for analysis and discussion.

Introduction to Spatial Transcriptomic Data Analysis-Jenny Wu, PhD

Computing on the HPC3 for Spatial Omics-Ivan Chang, PhD

Join us to learn key considerations for experimental design, and best practice guidance for successful sample preparation when you perform single cell gene expression analysis. Follow with your individual experimental design session.

If you would like to schedule an individual session after the workshop, please contact Christine.Kao@10xgenomics.com.

Need Help Planning a Project? Got Technical Questions? Check Out Back to School Promotions and Come Chat with your Acct Manager & Field Application Scientist

Account Manager – Moira.Goegel@QIAGEN.com – 619-357-2259

Genomics Field Application Scientist Matt.Collin@QIAGEN.com – 909-201-3728

Sign up for your individual session to discuss how the latest advancement in Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x 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@10xgenomics.com to schedule an appointment.

Need Help Planning a Project? Got Technical Questions? Check Out Back to School Promotions!

Come Chat with your Acct Manager & Field Application Scientist.

When: Thursday, September 12, 12:00-2:00 p.m.
Where: Sprague Hall Courtyard

Account Manager
Moira.Goegel@QIAGEN.com
619-357-2259

Genomics Field Application Scientist
Matt.Collin@QIAGEN.com
909-201-3728

The GRT Hub provides services and advanced tools like CytAssist for Visium, VisiumHD, and Xenium for In Situ Analysis, supporting research at UCI and beyond. Unlocking new insights into the spatial context of disease requires both depth and breadth. Depth gives researchers as much information as possible on each gene. Breadth provides a broader picture of biology with analysis of more genes. The NEW Xenium Prime 5K pan tissue & pathways assays allow researchers to get the best of both worlds to better understand complex biological phenomena with ultra-precise single cell spatial imaging for 5,000 genes. Join 10x Genomics and the GTR Hub to learn how the Xenium Prime 5K gene panel can elevate your research and offer new insights into the spatial context of diseases. Attendance is free, but registration is required.

Event Highlights:
● Discover the capabilities and applications of the Xenium Prime 5K gene panel.
● Networking & Free Breakfast!
● Attendees will receive special discounts on Xenium 5K.

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.

Sign up for your individual session to discuss how Chromium Single Cell, Visium Spatial, and Xenium In Situ platforms from 10x 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@10xgenomics.com to schedule an appointment.

The submission window is now open!

We encourage scientists of any level to apply! Simply complete the short form on this page and include your 100-word proposal. You can read the official rules or reach out if you have any questions about this Microbial Genomics SMRT Grant.

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