Gene expression at single-cell resolution – Course and Conference Office

EMBL Course

Gene expression at single-cell resolution


The course will be held online.

Course overview

The goal of this course is to provide participants with both the theory and practical skills required to design, prepare, run and analyse high-throughput single cell transcriptomic experiments using the Chromium Single Cell Controller from 10x Genomics. We will begin with a general introduction on the topic, including the cell partitioning technology, fundamentals of NGS, and the library preparation workflow. The hands-on session starts with cell handling followed by the preparation of transcriptome libraries from single-cells with a focus on best practices. Finally, we will quantify and quality control the prepared libraries, before sequencing on a NextSeq instrument. The final day will be dedicated to single-cell data analysis with a mixture of theory and hands-on experience using the Loupe Cell Browser from 10x Genomics.


This course is directed towards biologists, scientists and technicians who want to apply single-cell transcriptome sequencing and learn the basics of library preparation. Knowledge of next generation sequencing technology and cell culture is desirable but not essential.


  • Preparation of high-quality single-cell suspensions, flow cytometry
  • Best practices and “tips and tricks” for preparation of 3’-tagged RNA-Seq libraries from single cells for whole transcriptome gene expression analysis
  • Best practices of sequencing library validation
  • Introduction to single cell transcriptome data analysis

Learning outcomes

After this course you should be able to:

  • Prepare libraries from cell cultures for single-cell whole transcriptome analysis
  • Apply quality controls and library quantification
  • Know the basics of single-cell transcriptome data analysis

What past participants say about the course:

“This was a fantastic course that deepened my understanding of single-cell sequencing techniques. Additionally, the perfect blend of theoretical and practical sessions kept me engaged throughout. I am sure that the training I received will be immensely helpful as I look to expand my skillset in the burgeoning single-cell sequencing field. I definitely recommend this course to anyone interested in learning and gaining hands-on experience in single-cell sequencing.” – Niels Menezes, University of Copenhagen, Denmark

Speakers and Trainers

Simone Picelli

Institute of Molecular and Clinical Ophthalmology Basel


Scientific Organisers

Course Organisers


Got something to say? Tweet it with #EMBLscSeq

  • The virtual course will start on Monday 28 March 2022 with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on  Monday 4 April 2022 with the regular programme.
  • Participants will be required to view the pre-recorded talks prior to the main start of the course on Monday 4 April 2022. During the 5-day course duration, full-time attendance is required.  

All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and date along with your city into the Time Zone Converter.

This programme may be subject to change.

Day 0 – Monday 28 March 2022
14:00 – 15:00Onboarding
Day 1 – Monday 4 April 2022
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:15Welcome, House Notes and Course Overview
13:15 – 14:30Icebreaker (e.g. flashtalks)
14:30 – 14:45Break
14:45 – 15:15Live talk “Lecture: Introduction to 10X Single Cell 3′ Application
Specialist from 10x Genomics
15:15 – 15:45Speed networking break
15:45 – 16:15Live Q&A Session based on pre-recorded talk “Lecture: Illumina Sequencing Overview
Vladimir Benes – EMBL Heidelberg, Germany
Day 2 – Tuesday 5 April 2022
09:30 – 11:00Project Consultancy 1-on-1 (optional)
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk “Lecture: Sample Preparation Guide”
Diana Ordoñez-Rueda – EMBL Heidelberg, Germany
13:30 – 14:30Lecture: 10X Online Resources
Specialist from 10x Genomics
14:30 – 14:45Break
14:45 – 15:30Live Q&A Session based on pre-recording “Practical Session: Tips and Tricks Cell & Tissue Preparation & QC
15:30 – 16:00Fun Quiz Break
16:00 – 16:45Live Practical Session: Getting started with the Chromium Next GEM Single Cell 3ʹWorkflow Tips and Tricks- best practice
Specialist from 10x Genomics
Day 3 – Wednesday 6 April 2022
09:30 – 10:00Project Consultancy 1-on-1 (optional)
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk “Lecture: Ultrafast and Highly Sensitive Full-Length Single-Cell RNA-Sequencing using FLASH-Seq”
Simone Picelli – Institute of Molecular and Clinical Ophthalmology Basel (IOB), Switzerland
13:30 – 14:00Live Q&A Session based on pre-recorded talk “Lecture: A mosaic in the spinal cord: tackling motor neuron diversity”
Emanuela Zuccaro- University of Padova, Italy
14:00 – 14:15Break
14:15 – 15:00Live Q&A Session based on pre-recorded workflow tutorials “Practical Session: Continuing Chromium Next GEM Single Cell 3ʹWorkflow Tips and Tricks- best practice
15:00 – 15:30Break
15:30 – 16:00Practical Session: Self- Assessment of learned workflow via quiz
16:00 – 17:00Lecture: 10X Analysis Pipelines
Specialist from 10x Genomics
Day 4 – Thursday 7 April 2022
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:45Practical: Show and Tell Loupe Browser User Interface
Specialist from 10x Genomics
13:45 – 14:15Break
14:15 – 15:15Practical Hands-on Loupe Dataset
Specialist from 10x Genomics
15:15 – 15:30Break
15:30 – 16:15Solution room: Loupe Browers group assignment
Specialist from 10x Genomics
16:15 – 16:45Project Consultancy 1-on-1 (optional)
Day 5 – Friday 8 April 2022
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 14:00Live talk “Lecture: Primer to Illumina Data Analysis”
Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany
14:00 – 14:15Break
14:15 – 15:30Practical: Sequencing data Quality control
Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany
15:30 – 16:00Speed networking
16:00 – 16:45Practical: Experimental design tips and tricks
Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany
16:45 – 17:15Course wrap up

Practical Information

Registration Fees and Motivation Letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.


Registration Fees (include admission and all course materials):

PhD Student€295

Confirmation and Payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation Letter Submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.

Further Details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal. Read the instructions on how to apply for financial assistance.

Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.


The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

Check out this list of external funding opportunities or get more information on attending the conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Technical Requirements

Technical Requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.


The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other Information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Additional Information

Please find additional information including FAQs and terms and conditions on our Information for Participants page.


Sponsorship Opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Date: 4 - 8 Apr 2022

Location: Virtual


Application: Closed