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In collaboration with Project Jaguar, ICMT Universidad CES and Universidad de Antioquia, we are excited to offer a complimentary workshop on applying single-cell genomic techniques to investigate the immune system. Single-cell immunogenomics approaches help to understand how environmental factors and genetic backgrounds influence immune responses. This course is designed to equip scientists with the skills and resources to obtain and analyse single-cell omics data. We will highlight the interplay between experimental design, laboratory processing, and downstream analysis, sharing insights from our experiences in profiling the immune system and conducting in vitro stimulations.
In this course we will cover a toolkit of single-cell technologies, including scRNAseq, CITEseq, ATACseq, and immune receptor repertoires in single cell, discussing their benefits, limitations, and best practices. Additionally, we will share our experiences from a large-scale single-cell immunogenomics project involving researchers from various institutions based in seven Latin American countries working in partnership with Wellcome Sanger Institute (Project JAGUAR).
This course will be held preceding the ISCB Latin America Conference on Bioinformatics.
Early and mid-career biomedical scientists, MSc, PhD students and postdocs, who are beginning or planning to begin single-cell omics research in the field of immunology, are invited to participate. This course is open to applicants based in Latin America.
A basic proficiency in R or Python is required. Pre-course materials on R and Linux will be provided to prepare participants for the course.
What will you be able to do?
After attending this course, participants will be able to:
- Identify critical decisions for the data interpretability in their experimental planning and design with a focus on the immune system.
- Decide the appropriate steps for dataset preprocessing and analysis and apply them within the framework for immunological interpretation.
- Operate both R and Python-based analytical frameworks to conduct single-cell analysis.
- Understand the integration of samples and omics datasets e.g. transcriptomics and CITE-seq, across single cell experiments and how to leverage and interpret the results.
- Describe downstream analysis types appropriate for their biological questions in studying the immune system.
This hands-on bioinformatics workshop will offer a series of lectures and practical sessions covering the following topics:
- Single-cell basics and immune system applications: From the technology to the implementations.
- Best practices for experimental planning and design focusing on the study of the immune system.
- Single-cell RNA sequencing: from raw sequences to count matrix and downstream analysis through comprehensive data workflows.
- Immune receptor repertoires in single-cell technologies.
- CITE-seq technology to profile cells at transcriptomics and proteomic levels.
- ATAC-seq and multiome analysis.
Scientific Organising Committee
- Yesid Cuesta Astroz, University of Antioquía, Colombia
- Gosia Trynka, Wellcome Sanger Institute, UK
Course Instructors
- Anna (Ania) Lorenc, Wellcome Sanger Institute, UK
- Benilton Carvalho, UNICAMP, Brazil
- Carla Jones, Wellcome Sanger Institute, UK
- Danilo Ceschin, CIMETSA - IUCBC, Argentina
- Diego Ramirez, UNAM, Mexico
- Evelia Coss, UNAM, Mexico
- Felipe Gajardo, PUC, Chile
- Julieth Lopez, UNAL, Colombia
- Lucia Ramirez, Wellcome Sanger Institute, UK
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Isabela Malta, Assistant Global Training Manager
- Karon Chappell, Event Organiser
- Jorge Batista da Rocha, Laboratory Operations Officer
- Martin Asltett, Education Developer
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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