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Gene expression at spatial resolution – Course and Conference Office

EMBL Course

Gene expression at spatial resolution

Overview

Course overview

This interactive course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. Objectives The Visium Cytassist Spatial Gene Expression Solution uses probes targeting the whole transcriptome for intact tissue sections in morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Cytassist Spatial Gene Expression slides. Through practical work in the lab and theoretical sessions, the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training in spatial transcriptomics data analysis.

Audience

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 Cytassist Spatial Gene Expression application into their labs/research.

Modules / Resources

  • Overview of 10x Genomics Visium Cytassist Spatial Gene Expression technology
  • Focusing on fresh-frozen samples with Hematoxylin and Eosin (H&E) staining
  • Alternative staining by Immunofluorescence and usage of FFPE samples as starting material
  • Pre-recorded application lectures on Spatial Transcriptomics
  • Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
  • Visium Spatial Gene Expression data analysis using Loupe Browser (license-free)
  • 1-on-1 Project Consultation with application specialist (optional service offered at the discretion of the individual participant)

Learning Outcomes

After this course you will be able to:   

  • Appreciate the importance of spatially resolved transcriptomics data
  • Realise the significance of properly prepared tissue sections by cryosectioning
  • Understand the requirements for brightfield and fluorescent tissue slide imaging
  • Analyse and interpret data output using Loupe Browser

Speakers

Speakers / trainers

Ahmad Al Alwash

EMBL Heidelberg

Germany

Monika Dabrowska

10x Genomics

United Kingdom

Linda Decker

EMBL Heidelberg

Germany

Anna Klemm

SciLifeLab and Uppsala University

Sweden

(Virtual Speaker)

Mireia Osuna Lopez

EMBL Heidelberg

Germany

Kristy Ou

EMBL Heidelberg

Germany

Valeriy Pak

EMBL Heidelberg

Germany

Idoia Quintana Urzainqui

EMBL Heidelberg

Germany

Sinem Saka

EMBL Heidelberg

Germany

Oliver Stegle

EMBL Heidelberg

Germany

Laura Villacorta

EMBL Heidelberg

Germany

Scientific organisers

Dirk Jürgensen

10x Genomics

Germany

Course organisers

Sophie Dutzi

Course and Conference Officer

EMBL Heidelberg

Germany

Programme

Are you on social media? Post using #EMBLSpatialOmics and don’t forget to tag @EMBLEvents

  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday 4 March 2024
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
08:45 – 09:00RegistrationCourtyard Room A&B
09:00 – 09:30Welcome and house notes and course overviewCourtyard Room A&B
09:30 – 10:30Flash talk session
Courtyard Room A&B
10:30 – 11:00Coffee BreakCourtyard Room A&B
11:00 – 12:00Lecture 1: Introduction to the Visium Spatial Gene Expression Workflow
Dirk Jürgensen – 10x Genomics, Germany
Courtyard Room A&B
12:00 – 13:00LunchEMBL Canteen
13:00 – 15:30Practical session 1: Sample fixation, staining and probe hybridization
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training Lab A&B
15:30 – 16:00Coffee breakCourtyard Room A&B
16:00 – 18:00CryoStat demo session/ ALMF tour and imaging
Monika Dabrowska – 10x Genomics, UK
Ahmad Al Alwash – EMBL Heidelberg, Germany
Linda Decker – EMBL Heidelberg, Germany
DB unit/ALMF
18:00 – 19:00Lecture 2: Imaging good practices
Ahmad Al Alwash – EMBL Heidelberg, Germany
Courtyard Room A&B
19:00 – 20:00DinnerEMBL Canteen
20:00Departure to HotelATC Entrance
Day 2 – Tuesday 5 March 2024
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:05Overview of the dayTraining Lab B
09:05 – 10:05Practical session 2: Post Hybridzation Wash & Probe Ligation
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training Lab B
10:05 – 11:05Lecture 3: Title to be confirmed
Sinem Saka – EMBL Heidelberg, Germany
Courtyard Room A&B
11:05 – 12:05Practical session 3: Post ligation wash
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training Lab B
12:05 – 13:05LunchEMBL Canteen
13:05 – 17:05Practical session 4: Cytassist sessionTraining Lab B
17:05 – 17:35Practical session 5: Probe extension
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
17:35 – 18:35Lecture 4: Rubbish In Equals Rubbish Out: The Importance of Sample Quality
Monika Dabrowska – 10x Genomics, UK
Courtyard Room A&B
18:35 – 19:35DinnerEMBL Canteen
19:35Departure to HotelATC Entrance
Day 3 – Wednesday 6 March 2024
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:05Overview of the dayTraining lab B
09:05 – 10:35Practical session 6: Probe elution and pre-amplification
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
10:35 – 10:50Coffee breakCourtyard Room A&B
10:50 – 11:50Practical session 7: SPRI beads clean-up
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
11:50 – 12:50Lunch and course group photoEMBL Canteen
12:50 – 13:50Lecture 5: Studying the shark embryo to understand the cellular origin and evolution of the vertebrate brain
Idoia Quintana Urzainqui – EMBL Heidelberg, Germany
Courtyard Room A&B
13:50 – 14:05Coffee breakCourtyard Room A&B
14:05 – 15:05Practical session 8: qPCR – cycle number determination
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training lab B
15:05 – 16:05Lecture 6: Title to be confirmed
Oliver Stegle – EMBL Heidelberg, Germany
Courtyard Room A&B
16:05Free evening
16:05Departure to HotelIn front of ATC entrance
16:25Bus to NeckarmünzplatzBus stop in front of ISG Hotel
Day 4 – Thursday 7 March 2024
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 09:20Practical Lecture 7: qPCR results explained
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Courtyard Room A&B
09:20 – 10:00Practical session 9: Index PCR
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training Lab B
10:00 – 10:30Coffee breakCourtyard Room A&B
10:30 – 11:30Practical session 10: Final clean-up and QC
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Training Lab B
11:30 – 12:30Lecture 8: Title to be confirmed
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard Room A&B
12:30 – 13:30LunchEMBL Canteen
13:30 – 13:50Practical Lecture 9: Bioanalyzer results explained
Ahmad Al Alwash – EMBL Heidelberg, Germany
Monika Dabrowska – 10x Genomics, UK
Dirk Jürgensen – 10x Genomics, Germany
Fabio Marsoner – 10x Genomics, The Netherlands
Mireia Osuna Lopez – EMBL Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Courtyard Room A&B
13:50 – 15:50CryoStat demo session/ ALMF tour and imaging
Monika Dabrowska – 10x Genomics, UK
Ahmad Al Alwash – EMBL Heidelberg, Germany
Linda Decker – EMBL Heidelberg, Germany
DB unit/ALMF
15:50 – 16:05Coffee break
Courtyard Room A&B
16:05 – 17:30Practical lecture and demo 10: – Loop Browser and Space ranger
Dirk Jürgensen – 10x Genomics, Germany
Courtyard Room A&B
17:30 – 18:00Departure to Hotel and DowntownIn front of ATC entrance
18:00 – 19:30Free Time in the City Centre
19:30 – 22:00Course dinner downtown
Day 5 – Friday 8 March 2024
Time (Europe/Berlin)ProgrammeLocation
08:40 – 09:00Bus from hotel to EMBL ATC EntranceBus stop in front of ISG Hotel
09:00 – 10:30Practical session 11: Data analysis
Ahmad Al Alwash – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Valeriy Pak – EMBL Heidelberg, Germany
Computer Training Lab
10:30 – 11:00Coffee breakComputer Training Lab
11:00 – 12:00Practical session 12: Data analysis
Ahmad Al Alwash – EMBL Heidelberg, Germany
Kristy Ou – EMBL Heidelberg, Germany
Valeriy Pak – EMBL Heidelberg, Germany
Computer Training Lab
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:00Lecture 11: Evaluating Spatial Omics Data
Anna Klemm – SciLifeLab and Uppsala University, Sweden
(virtual talk)
Courtyard Room A&B
14:00 – 14:15Coffee breakComputer Training Lab
14:15 – 14:45Course wrap upCourtyard Room A&B
14:45Departure ATC entrance

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

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.

Academia€715
PhD Student€715
Industry€1225

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed.

We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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.

Instructions

  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 detailed instructions, please watch 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

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

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

This grant covers costs related to your attendance at 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

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding 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 the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Hotel

Single rooms have been reserved for 5 nights (3 – 8 March 2024) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code SPA24-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

Event software

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. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

Sponsors

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 events, 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.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 4 - 8 Mar 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

  • Vladimir Benes
    EMBL Heidelberg, Germany

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