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FISHing for RNAs: Classical to Single Molecule Approaches – Course and Conference Office

EMBO Practical Course

FISHing for RNAs: Classical to Single Molecule Approaches

Overview

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.

Course Overview

Over the past decades it became evident that a RNA transcripts specific amount and localisation are important in order to understand the biological function of its (non-) coding gene. Whereby state-of-the-art in situ hybridisation (ISH) technologies are key to visualise these RNAs in a given tissue or cell.

This course aims to highlight three powerful RNA visualisation techniques in histological tissue samples. During this course, the participants will learn to validate the cellular localisation of candidate genes from transcriptome studies through conventional ISH and, the more recent cutting-edge, smFISH (Single Molecule Fluorescent ISH) and HCR-ISH (Hybridization Chain Reaction), based RNA ISH hybridisation methods. Additionally, the course will also cover essential tissue embedding protocols that are adapted for use in visually interrogating RNA transcripts in mammalian tissues.

Audience

This course is directed to early stage scientists (PhD and Postdocs) from the fields of RNA and molecular biology as well as various fields with an interest in these methodologies.

Participant Commitment

  • The virtual course will start on Monday 12 July 2021, with an onboarding session and access to the pre-recorded lectures and pre-course study materials (exercises, assignments, etc.). It will continue on Monday 26 July 2021 with the regular programme.
  • The virtual course includes recorded / live lectures, interactive discussion sessions, online practicals, hands-on exercises, student presentations and networking.
  • Full-time attendance is required for the course duration.
  • Selected participants will have access to the recorded talks [1] week(s) before the start of the event. Please note that watching the recordings prior to the start of the course is required and will take approximately 6 – 8 hours.
  • Information on the live stream and access to the virtual course platform will be provided shortly before the start of the event.
  • Access to the recorded talks and the virtual course platform will be available for [1] week(s) after the end of the event.

Speakers and Trainers

Sara Di Persio

Centre of Reproductive Medicine and Andrology – University Hospital Münster

Germany

Imre Gaspar

Institute of Molecular Biotechnology

Austria

Ewa Piskadlo

Friedrich Miescher Institute for Biomedical Research

Switzerland

Scientific Organisers

Imre Gaspar

Institute of Molecular Biotechnology

Austria

Course Organisers

Maryann Heck

Deputy Head and Courses and Conferences Team Lead

EMBL Heidelberg

Germany

Tim Nürnberger

Courses and Conferences Team Lead

EMBL Heidelberg

Germany

Yvonne Yeboah

Training Laboratory Manager

EMBL Heidelberg

Germany

Programme

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  • The virtual course will include interactive discussion sessions, online practicals, hands on exercises and virtual networking.
  • Participants will be required to view the pre-recorded talks prior to the main start of the course on Monday, 26 July 2021. During the five-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.

Day 0 – Monday 12 July 2021
TimeSpeaker
12:00 – 14:00Onboarding and technical troubleshooting
Day 1 – Monday 26 July 2021
Time Speaker
12:45 – 13:00Check-in and overview of the day
13:00 – 13:15Welcome and house notes and course overview
13:15 – 14:30Icebreaker (e.g. flashtalks)
14:30 – 14:45Break
14:45 – 15:15Live Q&A session based on pre-recorded talk:
Histology overview and applications
Emerald Perlas – EMBL Rome, Italy
15:15 – 15:45Live Q&A session based on pre-recorded talk :
RNA detection methods
Imre Gaspar – Institute of Molecular Biotechnology, Austria
15:45 – 16:15Speed networking break
16:15 – 17:15Student presentations
Day 2 – Tuesday 27 July 2021
TimeSpeaker
12:45 – 13:00 Check-in and overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk
Differentially localised CDC42 mRNA isoforms
Marina Chekulaeva – Max Delbrück Center for Molecular Medicine, Germany
13:30 – 14:00Live Q&A Session based on pre-recorded talk
Tom Pollex – EMBL Heidelberg, Germany
14:00 – 14:15Break
14:15 – 15:00Live interactive practical:
Sample sectioning live lab demo
Emerald Perlas – EMBL Rome, Italy
15:00 – 15:30Break
15:30 – 16:00Live interactive practical continues :
Sample sectioning tips and tricks
Emerald Perlas – EMBL Rome, Italy
16:00 – 17:00Student presentations
Day 3 – Wednesday 28 July 2021
Time Speaker
12:45 – 13:00 Check-in and overview of the day
13:00 – 13:30Interactive practical:
Imaging conventional ISH- live Q&A to pre-recorded video
Emerald Perlas – EMBL Rome, Italy
13:30 – 14:00Live Q&A Session based on pre-recorded talk
Mainak Bose – EMBL Heidelberg, Germany
14:00 – 14:15Break
14:15 – 15:00Interactive practical:
Introduction to Probe design- LIve Q&A to pre-course assignment
Imre Gaspar – Institute of Molecular Biotechnology, Austria
15:00 – 15:30Break
15:30 – 16:00Interactive practical:
Introduction to Probe design- LIve Q&A to pre-course assignment
Imre Gaspar – Institute of Molecular Biotechnology, Austria
16:00 – 17:00Student presentations

Day 4 – Thursday 29 July 2021
Time Speaker
12:45 – 13:00 Check-in and overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk
Ewa Piskadlo – Friedrich Miescher Institute for Biomedical Research, Switzerland
13:30 – 14:00Interactive practical:
Single Molecule Fluorescent ISH workflow- FAQs
Imre Gaspar – Institute of Molecular Biotechnology, Austria
14:00 – 14:15Break
14:15 – 15:00Interactive practical :
Single Molecule Fluorescent ISH Imaging- Demo
Imre Gaspar – Institute of Molecular Biotechnology, Austria
15:00 – 15:30Break
15:30 – 16:00Live practical: continues
Single Molecule Fluorescent ISH Imaging- Demo
Imre Gaspar – Institute of Molecular Biotechnology, Austria
16:00 – 17:00Student presentations
Day 5 – Friday 30 July 2021
Time Speaker
12:45 – 13:00Check-in and overview of the day
13:00 – 13:30 Live Q&A Session based on pre-recorded talk or live session
ncRNA Charme in cardiac and skeletal muscle
Monica Ballarino – Sapienza University of Rome, Italy
13:30 – 14:15Live interactive discussion:
The solution Room:
Experts and peer supported advice on your most pressing problems
14:15 – 14:30Break
14:30 – 15:30Interactive practical:
Basics ISH image analysis- on provided data set
15:30 – 16:00Break
16:00 – 17:00Interactive practical:
Basics ISH image analysis-on provided data set
17:00 – 17:15Interactive Session: Course wrap – up session

– take away message for participants
– short feedback round
17:15Goodbye and end of course

Practical information

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 events in Heidelberg and will be indicated during the abstract or motivation letter submission process. A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

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

Virtual events: You are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting.

EMBO childcare grants are available for EMBO Practical Courses and Workshops at all EMBL sites.

Registration Fee Waiver

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

Childcare Grant (EMBO Practical Courses only)

For EMBO 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 baby-sitter or child-care facility, travel costs for a care giver, 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 EUR 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 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

Application

You may apply for financial assistance when submitting your motivation letter for courses, and abstract for conferences. 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 Inhelheim Fonds Fellowship, 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 or abstract 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 meeting. Selection is based on 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

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

Technical Requirements

Technical Requirements

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.

Virtual Participation Guidelines

Guidelines

Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Share Slack, live stream or poster session links with others
  • Broadcast the conference to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

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 events Slack workspace for you to enjoy during the event.

How to ask questions

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 Slack to ask your questions in the dedicated session channels or via direct message.

Time zone

The programme is planned based on Central European Time (CET), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accomodate as many timezones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Sponsors

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: 26 - 30 Jul 2021

Location: Virtual


Deadline(s):

Closed


Organisers:

  • Imre Gaspar
    Institute of Molecular Biotechnology, Austria

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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