Ahmad Al Alwash
EMBL Heidelberg
Germany
EMBL Course
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.
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.
After this course you will be able to:
EMBL Heidelberg
Germany
10x Genomics
United Kingdom
EMBL Heidelberg
Germany
SciLifeLab and Uppsala University
Sweden
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
10x Genomics
Germany
EMBL Heidelberg
Germany
Course and Conference Officer
EMBL Heidelberg
Germany
Training Lab Technician
EMBL Heidelberg
Germany
Are you on social media? Post using #EMBLSpatialOmics and don’t forget to tag @EMBLEvents
Time (Europe/Berlin) | Programme | Location |
---|---|---|
08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | Bus stop in front of ISG Hotel |
08:45 – 09:00 | Registration | Courtyard Room A&B |
09:00 – 09:30 | Welcome and house notes and course overview | Courtyard Room A&B |
09:30 – 10:30 | Flash talk session | Courtyard Room A&B |
10:30 – 11:00 | Coffee Break | Courtyard Room A&B |
11:00 – 12:00 | Lecture 1: Introduction to the Visium Spatial Gene Expression Workflow Dirk Jürgensen – 10x Genomics, Germany | Courtyard Room A&B |
12:00 – 13:00 | Lunch | EMBL Canteen |
13:00 – 15:30 | Practical 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 – 16:00 | Coffee break | Courtyard Room A&B |
16:00 – 18:00 | CryoStat 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 – 19:00 | Lecture 2: Imaging good practices Ahmad Al Alwash – EMBL Heidelberg, Germany | Courtyard Room A&B |
19:00 – 20:00 | Dinner | EMBL Canteen |
20:00 | Departure to Hotel | ATC Entrance |
Time (Europe/Berlin) | Programme | Location |
---|---|---|
08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | Bus stop in front of ISG Hotel |
09:00 – 09:05 | Overview of the day | Training Lab B |
09:05 – 10:05 | Practical 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 – 11:05 | Lecture 3: A DNA toolbox for spatial biology Sinem Saka – EMBL Heidelberg, Germany | Courtyard Room A&B |
11:05 – 12:05 | Practical 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 – 13:05 | Lunch | EMBL Canteen |
13:05 – 17:05 | Practical session 4: Cytassist session | Training Lab B |
17:05 – 17:35 | Practical 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 – 18:35 | Lecture 4: Rubbish In Equals Rubbish Out: The Importance of Sample Quality Monika Dabrowska – 10x Genomics, UK | Courtyard Room A&B |
18:35 – 19:35 | Dinner | EMBL Canteen |
19:35 | Departure to Hotel | ATC Entrance |
Time (Europe/Berlin) | Programme | Location |
---|---|---|
08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | Bus stop in front of ISG Hotel |
09:00 – 09:05 | Overview of the day | Training lab B |
09:05 – 10:35 | Practical 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 – 10:50 | Coffee break | Courtyard Room A&B |
10:50 – 11:50 | Practical 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 – 12:50 | Lunch and course group photo | EMBL Canteen |
12:50 – 13:50 | Lecture 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 – 14:05 | Coffee break | Courtyard Room A&B |
14:05 – 15:05 | Practical 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 – 16:05 | Lecture 6: Title to be confirmed Oliver Stegle – EMBL Heidelberg, Germany | Courtyard Room A&B |
16:05 | Free evening | |
16:05 | Departure to Hotel | In front of ATC entrance |
16:25 | Bus to Neckarmünzplatz | Bus stop in front of ISG Hotel |
Time (Europe/Berlin) | Programme | Location |
---|---|---|
08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | Bus stop in front of ISG Hotel |
09:00 – 09:20 | Practical 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 – 10:00 | Practical 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 – 10:30 | Coffee break | Courtyard Room A&B |
10:30 – 11:30 | Practical 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 |
11:45 – 12:30 | Lunch | EMBL Canteen |
12:30 – 13:30 | Lecture 8: NGS – an end point or a new beginning? Vladimir Benes – EMBL Heidelberg, Germany | Courtyard Room A&B |
13:30 – 13:50 | Practical 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 – 15:50 | CryoStat 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 – 16:05 | Coffee break | Courtyard Room A&B |
16:05 – 17:30 | Practical lecture and demo 10: – Loop Browser and Space ranger Dirk Jürgensen – 10x Genomics, Germany | Courtyard Room A&B |
17:30 – 18:00 | Departure to Hotel and Downtown | In front of ATC entrance |
18:00 – 19:30 | Free Time in the City Centre | |
19:30 – 22:00 | Course dinner downtown |
Time (Europe/Berlin) | Programme | Location |
---|---|---|
08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | Bus stop in front of ISG Hotel |
09:00 – 10:30 | Practical 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 – 11:00 | Coffee break | Computer Training Lab |
11:00 – 12:00 | Practical 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 – 13:00 | Lunch | EMBL Canteen |
13:00 – 14:00 | Lecture 11: Evaluating Spatial Omics Data Anna Klemm – SciLifeLab and Uppsala University, Sweden | Courtyard Room A&B |
14:00 – 14:15 | Coffee break | Computer Training Lab |
14:15 – 14:45 | Course wrap up | Courtyard Room A&B |
14:45 | Departure | ATC entrance |
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, 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.
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 detailed instructions, please watch 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.
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.
The fee waiver will cover the registration sum that you have paid to attend the course.
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.
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.
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
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.
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.
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
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.
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.
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.
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.
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 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
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.
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.
Date: 4 - 8 Mar 2024
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
Contact: Sophie Dutzi