Alma Andersson
Science for Life Laboratory
Sweden
EMBL Course
EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.
This interactive virtual course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. The Visium Spatial Gene Expression Solution incorporates unbiased, high-throughput total mRNA analysis for intact tissue sections with morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Spatial Gene Expression slides. Through theoretical and interactive sessions as well as remote demonstrations of some of the practical work in the lab, the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and optimisation of tissue permeabilisation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training of spatial transcriptomics data analysis.
This is an interdisciplinary course designed for molecular biologists as well as researchers more familiar with morphology analysis by brightfield and fluorescence microscopy who are seeking to introduce the 10x Genomics Visium Spatial Gene Expression application into their labs/research.
During this course we will cover the following aspects:
After this course you will be able to:
Science for Life Laboratory
Sweden
10x Genomics
France
10x Genomics
Sweden
10x Genomics
Germany
10x Genomics
Sweden
10x Genomics
Sweden
Uniklinik RWTH Aachen
Germany
Medical Center – University of Freiburg
Germany
EMBL Heidelberg
Germany
10x Genomics
Germany
EMBL Heidelberg
Germany
10x Genomics
Germany
EMBL Heidelberg
Germany
Course and Conference Officer
EMBL Heidelberg
Germany
Course and Conference Officer
EMBL Heidelberg
Germany
Training Lab Manager
EMBL Heidelberg
Germany
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Time | Live session |
---|---|
13:00 – 14:00 | Onboarding session |
Time | Live sessions |
---|---|
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 | Ice breaker – flash talks |
14:30 – 14:45 | Break |
14:45 – 15:45 | Introduction to the Visium Spatial Gene Expression Workflow Natalia Anahi Juiz, 10x Genomics, France |
15:45 – 16:15 | Speed Networking Break |
16:15 – 17:15 | Tissue Sample Preparation Erika Urdaneta, 10x Genomics, Germany |
Time | Live sessions |
---|---|
10:30 – 10:30 | Project Consultancy 1-on-1 (optional) |
10:30 – 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: An orientation in the spatial transcriptomics landscape Alma Andersson, SciLifeLab, Sweden |
13:30 – 14:00 | Live Q&A Session based on pre-recorded talk Sinem K. Saka, EMBL Heidelberg, Germany |
14:00 – 14:30 | Quiz time |
14:30 – 15:30 | Troubleshooting the Workflow Katharina Danielski, 10x Genomics, Germany |
15:30 – 16:30 | Getting started with the Visium FFPE Workflow Adam Jeraud, 10x Genomics, Germany |
Time | Live sessions |
---|---|
10:30 -10:30 | Project Consultancy 1-on-1 (optional) |
10:30 – 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: Whole-Transcriptome Spatial Mapping of the Healthy and Infarcted Human Heart Christoph Kuppe, Uniklinik RWTH Aachen, Germany |
13:30 – 14:00 | Live Q&A Session based on pre-recorded talk: Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma Vidhya Ravi, Medical Center, University of Freiburg, Germany |
14:00 – 14:15 | Break |
14:15 – 14:45 | Live Q&A Session based on pre-recorded talk: Visium Spatial Gene Expression Solution Software Training – Space Adam Jerauld, 10x Genomics, Sweden |
14:45 – 15:15 | Break |
15:15 – 16:15 | Interactive Session: Loupe Browser Adam Jerauld, 10x Genomics, Sweden |
Time | Live sessions |
---|---|
12:45 – 13:00 | Check-in Participants and Overview of the day |
13:00 – 14:00 | Live Lab Session: Cryosectioning Adam Jerauld, 10x Genomics, Sweden Aleksandra Jurek, 10x Genomics, Sweden |
14:00 – 14:15 | Break |
14:15 – 15:15 | Live Lab session: Microscope Adam Jerauld, 10x Genomics, Sweden James Chell, 10x Genomics, Sweden |
15:15 – 15:45 | Break |
15:45 – 16:15 | Interactive Session: Course Wrap Up Session |
16:15 | Goodbye and End of Course |
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:
Academia | 295 Euro |
PhD student | 295 Euro |
Industry | 520 Euro |
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:
Motivation letter length: The maximum limit of 2000 characters (ca. 200 words) refers to manually typed text (spaces included).
Free field text length: The maximum characters for your answers in the free field text boxes is 255 (spaces included). Text only: If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:
Symbols: If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.
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 by following the instructions here. 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.
A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.
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 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 do:
Please don’t:
Additional information can be found in our Code of Conduct.
It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the eCampus for you to enjoy during the event.
Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use eCampus to ask your questions in the dedicated Forum or via direct message.
The programme is planned based on Central European Summer Time (CEST), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accommodate as many time zones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.
Course Sponsor
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: 30 Aug - 2 Sep 2021
Location: Virtual
Deadline(s):
Registration: Closed
Organisers:
Contact: Iva Gavran