Workshops

Sign up for your individual session to discuss how the latest advancements 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. We hope to see you and learn about your research!

Please email christine.kao@10xgenomics.com to schedule an appointment.

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.

Here are some updates from 10x, please email christine.kao@10xgenomics.com to
schedule an appointment.

CRISPR Screening w/ GEM-X Flex

● Profile tens to thousands of sgRNAs simultaneously
● Directly link CRISPR edits and gene expression phenotypes at single cell resolution
● Per sample costs between $380 – $700 when multiplexing (min of 4 samples)

Visium HD 3′ – Pre-order available now!
● Species agnostic single cell scale spatial transcriptomics platform
● Compatible with Fresh Frozen and Fixed Frozen tissues
● >30 tissue types tested to date
● Limited transcript diffusion
GEM-X Universal 3′ & 5′ – On Chip Multiplexing

● Load 4 individual samples per chip
● Capture 5k cells per barcoded sample
● Gel beads contain sample ID so that multiplexing can happen on the chip and during the instrument run
● $560 per sample

In this hands-on workshop, you’ll embark on the Visium HD Spatial Gene Expression data analysis journey with us. Using example human colon cancer sample data , we’ll begin by processing raw data with Space Ranger on the 10x Cloud Analysis platform. Next, we’ll assess data quality using the web summary and then dive into Loupe Browser for in-depth data exploration and cell-type mapping. We’ll then take these insights to community-developed tools, further exploring the tumor microenvironment through pathway analysis. To conclude, each participant will have the opportunity to discuss their own analysis roadmap with guidance from 10x Genomics experts. Even though this workshop is focused on Visium HD Spatial Gene data, parts of the workshop will also be useful for single cell experiments

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 your one-on-one appointment

Click HERE for information for UCI attendees on parking and ride shares

In these trying times of threatened funding cuts, federal firings and science censorship, there is an argument to be made that scientists need to display some solidarity.   

This workshop will introduce the applications of statistical and data science methods towards genomics including generalized linear models in count data, pathway analysis, and imaging data analysis. We will review basic concepts in statistics and machine learning, supervised and unsupervised modeling, and generative vs. discriminative approaches. A hands-on session is emphasized and will showcase how to use R and Python to perform common analysis tasks in genomics. Attendees are encouraged to bring their own project data for analysis and discussion. Instructors: Jenny Wu, PhD and Ivan Chang, PhD

Introduction To Statistics In Genomics – Jenny Wu, PhD

Machine Learning In Imaging Data Using Python – Ivan Chang, PhD

Machine Learning in Imaging Data Using Python – Ivan Chang, PhD

Stop by and talk with PacBio scientists about current projects, help scoping future ones, or learn about the latest advances in whole genome sequencing, long read RNA-Seq, and native methylation detection. Coffee and snacks will be provided!

Reserve a specific time slot by emailing awestman@pacb.com

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 your one-on-one appointment

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