Vladimir Benes
EMBL Heidelberg
Germany
EMBL Course
The course will be held online.
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.
After this course you should be able to:
“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
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
10x Genomics
The Netherlands
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
Institute of Molecular and Clinical Ophthalmology Basel
Switzerland
10x Genomics
The Netherlands
10x Genomics
Germany
University of Padova
Italy
EMBL Heidelberg
Germany
10x Genomics
The Netherlands
EMBL Heidelberg
Germany
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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.
Time | Session |
---|---|
14:00 – 15:00 | Onboarding |
Time | Session |
---|---|
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 13:15 | Welcome, House Notes and Course Overview |
13:15 – 14:30 | Icebreaker (e.g. flashtalks) |
14:30 – 14:45 | Break |
14:45 – 15:15 | Live talk “Lecture: Introduction to 10X Single Cell 3′ Application“ Specialist from 10x Genomics |
15:15 – 15:45 | Speed networking break |
15:45 – 16:15 | Live Q&A Session based on pre-recorded talk “Lecture: Illumina Sequencing Overview“ Vladimir Benes – EMBL Heidelberg, Germany |
Time | Session |
---|---|
09:30 – 11:00 | Project Consultancy 1-on-1 (optional) |
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 13:30 | Live Q&A Session based on pre-recorded talk “Lecture: Sample Preparation Guide” Diana Ordoñez-Rueda – EMBL Heidelberg, Germany |
13:30 – 14:30 | Lecture: 10X Online Resources Specialist from 10x Genomics |
14:30 – 14:45 | Break |
14:45 – 15:30 | Live Q&A Session based on pre-recording “Practical Session: Tips and Tricks Cell & Tissue Preparation & QC“ |
15:30 – 16:00 | Fun Quiz Break |
16:00 – 16:45 | Live Practical Session: Getting started with the Chromium Next GEM Single Cell 3ʹWorkflow Tips and Tricks- best practice Specialist from 10x Genomics |
Time | Session |
---|---|
09:30 – 10:00 | Project Consultancy 1-on-1 (optional) |
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 13:30 | Live 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 – 14:00 | Live 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 – 14:15 | Break |
14:15 – 15:00 | Live 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 – 15:30 | Break |
15:30 – 16:00 | Practical Session: Self- Assessment of learned workflow via quiz |
16:00 – 17:00 | Lecture: 10X Analysis Pipelines Specialist from 10x Genomics |
Time | Session |
---|---|
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 13:45 | Practical: Show and Tell Loupe Browser User Interface Specialist from 10x Genomics |
13:45 – 14:15 | Break |
14:15 – 15:15 | Practical Hands-on Loupe Dataset Specialist from 10x Genomics |
15:15 – 15:30 | Break |
15:30 – 16:15 | Solution room: Loupe Browers group assignment Specialist from 10x Genomics |
16:15 – 16:45 | Project Consultancy 1-on-1 (optional) |
Time | Session |
---|---|
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 14:00 | Live talk “Lecture: Primer to Illumina Data Analysis” Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany |
14:00 – 14:15 | Break |
14:15 – 15:30 | Practical: Sequencing data Quality control Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany |
15:30 – 16:00 | Speed networking |
16:00 – 16:45 | Practical: Experimental design tips and tricks Jan Provaznik – EMBL Heidelberg, Germany; Jonathan Landry – EMBL Heidelberg, Germany |
16:45 – 17:15 | Course wrap up |
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):
Academia | €295 |
PhD Student | €295 |
Industry | €590 |
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.
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.
Instructions
Please note:
For more detailed information, follow the instructions provided in our video on how to submit a course motivation letter.
For further information about registration and motivation letter submission please refer to the FAQ page.
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.
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.
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.
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.
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.
While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.
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
Deadline(s):
Application: Closed
Organisers:
Contact: Lina Nikolajeva