Single-cell transcriptomic analysis training

Single-cell and single-nucleus analysis has emerged as a pivotal approach to investigate cellular heterogeneity and gain mechanistic insight into tendon health and disease. The TENET COST Action (CA22170) is pleased to invite applications for a three-day in-person training school on single-cell transcriptomic analysis. This workshop combines experimental and computational modules designed to provide participants with hands-on experience and conceptual understanding of cutting-edge single-cell workflows in tendon research.

Please note: This training is primarily designed for wet-lab scientists who require a foundational understanding of bioinformatics workflows. It is not intended as a specialized training course for bioinformaticians seeking to learn in-depth analysis of tendon tissue datasets.

Experimental Module

Participants will learn optimized procedures for processing both small and large tendon samples, including cell and nuclei isolation protocols suitable for downstream flow cytometry, single-cell and single-nuclei RNA sequencing.

Computational Module

The computational part introduces participants to best practices for experimental design and data analysis. Attendees will learn the principles of

• Preprocessing and quality control of single-cell data
• How seurat objects are generated
• Dataset integration and annotation
• How cell trajectory inference and cell–cell communication mapping can be applied to give functional insight to datasets

The content will be presented in the context of current research in the tendon field, enabling attendees to appreciate the specific nuances and challenges associated with tendon-derived datasets. The aim is to equip participants with the ability to critically evaluate tendon-related publications and to apply principles of robust experimental design to their own single-cell–resolution studies.

Please note: Basic knowledge of R is required for participation.

Learning goals

• Learn about different single cell technologies and how to decide on which to choose for your study
• Gain practical experience with nuclei and cell isolation from tendon tissues of various sizes
• Understand the key principles in single cell experimental design and data integration
• Learn best-practices for single- cell/nucleus RNA-seq bioinformatic analysis

Date

March 4th to 6th, 2026 (starting at 13.00 h on March 4th, for arrival)

Venue

VIB-UGent Center for Inflammation Research
Technologiepark-Zwijnaarde 71
9052 Zwijnaarde
Belgium

We recommend that participants book accommodation in central Ghent, where a variety of hotels and restaurants are within walking distance of public transportation station and historic center.

• ibis Gent Centrum St Baafs Kathedraal 
• NH Collection Gent
• Novotel Gent Centrum

Application process

Applicants are asked to submit a brief motivation letter (maximum 500 words) describing their interest in attending the workshop, the relevance and expected benefit for their current research project, and whether they are already applying or planning to apply single-cell or single-nucleus sequencing (sc/snSEQ) approaches in the near future. Applicants should also highlight how participation in the workshop could be beneficial for their scientific development and career progression. A short (2 page max) scientific CV must be included with the application. Applications must be submitted until December, 19^th at 23.59 pm (CET) using the ink provided below.

Please note that participation is limited to 15 attendees. Selection will be based on a scoring system evaluating motivation, relevance to ongoing or planned research, and potential for impact. Attendance will be restricted to 1 individual per research institution and priority will be given to junior researchers (PhD candidates and postdoctoral fellows, according to COST definition).

Reimbursement eligibility

Please note that travel expenses can only be reimbursed for active TENET members, within the limits detailed below:

• Daily allowances may be reimbursed for a maximum of one day prior to the start of the workshop and one day following its conclusion.
• A maximum daily allowance of EUR 200 applies per full day.
• Incurred long-distance travel expenses will be reimbursed on face-value including VAT, up to a maximum of EUR 500, cancellation insurance included, for the roundtrip.
• Participants are required to sign the official attendance list for each day they are present at the workshop. Participants are required to submit the travel expense reimbursement claim and relevant documentation in e-COST within 15 days after the end date of the event.
• Invitations to participants will be issued via e-COST, 30 days before the event start date. Participants should accept the e-COST invitation within 1 week from receiving it and register for in-person attendance.

Review the COST Travel Reimbursement Rules for additional information.