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EMBO Practical Course

Single cell genomics: Get started!

30 August – 05 September 2021 | Braga, Portugal

EMBO Childcare Grants Logo
  • Registration Deadline
  • 1 June 2021
  • Abstract Submission Deadline
  • 1 June 2021
  • Chosen Participants Will Be Notified By
  • 1 July 2021
  • Payment Deadline
  • 1 August 2021

Apply now!

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About the Practical Course

Single cell genomics techniques have recently emerged as a powerful tool and already revolutionized the way we think about tissue heterogeneity, cell identity and gene regulation. We are at the beginning of a new era where these techniques are becoming standards and are universally applied for broad phenotyping and to answer biomedical questions.
While this field is rapidly evolving and thriving driven by a core single cell omics community, the lack of expertise on these approaches hinders many Institutions and laboratories to take the leap. Despite the wealth of tools being developed, the toolset often become a jungle for the new comer: where should we start from? What is the best tool for the purpose? How can we be sure we are interpreting the results correctly?
This EMBO Practical Course will empower researchers to use single cell technologies in their labs with confidence. It will teach the basics of single cell experimental and computational workflows guiding the participant from the tissue handling to the computational analysis. We will demonstrate the most common applications: single cell/nucleus RNA-seq and single cell ATAC-seq, with focus not only on the possibilities opened, but also on the bottlenecks, limitations and the strategies to overcome them.


  1. Sample preparation (cells and nuclei) and protocol optimization
  2. Droplet-based single-cell/nucleus RNA-seq
  3. Droplet-based single-cell/nucleus ATAC-seq
  4. Computational analysis of NGS data from single-cell/nucleus RNA-seq
  5. Computational analysis of NGS data from single-nucleus ATAC-seq
  6. A guide to the interpretation of outputs and how to avoid common pitfalls
  7. Integrative OMICS – focus on transcriptome and epigenome


This courses seeks to facilitate the implementation of single-cell OMICS approaches in Institutions/labs by introducing the basics for its successful outcomes.

Our take home message is: “ Nobody is an expert to start with, just take the leap and let us guide you to become one”. In the end of the course we expect researchers to be able to perform transcriptomic and/or epigenomic experiments and be equipped with the tools to further develop their knowledge.







  • Registration Deadline
  • 1 June 2021
  • Abstract Submission Deadline
  • 1 June 2021
  • Chosen Participants Will Be Notified By
  • 1 July 2021
  • Payment Deadline
  • 1 August 2021



Registration includes:

  • Accommodation
  • All meals (apart from free evenings)
  • Local transport for dinners
  • Network activities


Selected participants will receive payment details by email. To complete the registration process, you should proceed with the payment and send the receipt to within 5 days.

Your registration will be effective after confirmation of payment. If payment is not concluded in due time we will have to cancel the registration.

Payment options:

  • Bank Transfer
  • ATM: The amount will be immediately debited from your account when paying at ATM or Home Banking;

Payment will be made in Euros €.

Selection criteria

Participants will be selected according to:

  • Their scientific merit evaluated by their CV and abstract
  • Their level of commitment to this course demonstrated by the motivation letter
  • Preference will be given to participants coming from Institutions and/or laboratories with little or no expertise in single cell genomics that are recently entering in this field and keen to learn and develop these skills beyond the course at their home Institutions/Labs.
  • Selection of candidates coming from the same Institutions and over-representing genders or countries will be avoided.

Abstract guidelines

The abstract is limited to 250 words and should summarize their current research work. It will be included in the course book.

Poster specifications

Posters boards are in portrait format, and posters size should be 120 cm x 70 cm (max).

Travel grants

A limited number of travel grants are available for participants. Applicants do not need to apply separately for travel grants for this event but should indicate on the registration form if they wish to be considered for a travel grant. Selection of awardees is handled directly by the organizer who will notify all eligible participants. More information is available at EMBO Travel Grants' page.

Specific travel grants and fee waivers are available for participants of any nationality working in laboratories in Chile, India, Singapore and Taiwan. To apply, please send an email directly to the meeting organisers justifying your request.

Child care grant

EMBO Courses and Workshops offers grants to offset additional child care costs incurred by participants or speakers when participating at any EMBO Courses and Workshop funded meeting. Eligible costs include fees for a caregiver or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please indicate on the registration form whether you would like to be considered for the grant. Please also describe how you intend to use the child care grant and specify the sum that you will need.



Ana Mendanha Falcão





Life and Health Sciences Research Institute (ICVS)

University of Minho

Campus Gualtar


Braga, Portugal


All participants will be housed together. Due to the pandemic situation we will house the participants in single rooms, when requested.

See accommodation details here:


Arrival by plane:

The closest airport is the international airport of Francisco Sá Carneiro in Porto which is less than an hour by bus shuttle (getbus: from Braga.

Transportation to Braga:

Train/Metro – Metro to Campanhã Station or São Bento Station followed by train to Braga.

Bus transfer – Direct transfer to Braga from Porto Airport and vice versa, everyday - “GET BUS"

Taxi – The taxis are located on the arrivals floor at Porto Airport.

Arrival by car: Rua 24 de Junho, 4715-051 Gualtar, Braga, Portugal

Coordinates: 41.55663, -8.39663

About the Area

The venue and accommodation are close to the city centre and to the world heritage site “Bom Jesus”, which is located at the top of the city of Braga offering an amazing view over the city and the surrounding area. The famous Bom Jesus is a Sanctuary with a monumental, Baroque stairway that climbs 116 meters, being one of the most famous attractions of Portugal.

Braga city is regarded as the religious center of Portugal, as it is the home of Portugal’s first bishop and earliest cathedrals. The city center is full of numerous churches, grand Baroque buildings and grand plazas. Is a city full of shops, restaurants and nightlife.

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