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Analysis and integration of transcriptome and proteome data – Cancelled – Course and Conference Office

EMBL Course

Analysis and integration of transcriptome and proteome data – Cancelled

Overview

Due to renewed restrictions related to the pandemic, we are unfortunately not able to host this course onsite. As a result, we are cancelling this course and apologise for the inconvenience.

Course Overview

Systems biology is a still expanding field of research aiming to understand at the molecular level how cells, tissues and organisms operate in their biological context. Among the key technologies driving this forward are next-generation sequencing and proteomics, as they provide powerful means to determine global expression levels of genes and proteins. Both fields have matured to a degree that they have now become accessible to researchers in many areas of biology. During this course, participants will gain theoretical insight in the structure of sequencing and proteomic data, and they will receive training in data analysis for the annotation, quantification and statistical analysis of gene and protein expression using various computational tools. In addition, training will be provided in the use of Cytoscape to derive biological insights from the integration of both data types.

Audience

This course is targeted at biologists and biochemists who are (starting to be) involved in both next-generation sequencing and mass spectrometry-based proteomics, but who are not experts in these fields.

Modules/Resources

  • Principles of mRNA quantification
  • Principles of protein identification and quantification
  • Principles and application of bioinformatic tools for mining of transcriptome and proteome data
  • Data integration by Cytoscape

Learning Outcomes

The aim of this practical course is to provide insight in techniques that are frequently used for transcriptome and proteome analysis, and to provide hands-on experience turning primary data into information that can be used for further biological interpretation. To achieve these goals, participants will gain insight in the basic principles of gene expression analysis (RNAseq data quantification and differential expression analysis), protein identification and quantification, and they will be trained in the use of software tools to analyse sequencing and proteomic data (SearchGUI, PeptideShaker, MaxQuant). In addition, the course will provide insight in the complementarity of transcriptome and proteome data by their integrative analysis via Cytoscape.

Speakers and Trainers

Speakers and Trainers

Scientific Organisers

Course Organisers

Maria Mercedes Bacadare Goitia

Course and Conference Manager

EMBL Heidelberg

Germany

Preliminary Programme

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  • Some pre-course work (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.
  • All times in the programme below are shown as the time in Europe/Berlin.

The preliminary programme below is a draft and is subject to change.

Day 1 – Sunday 6 March 2022
TimeSpeakerLocation
09:30 – 10:30Arrival, welcome and safety introductionsCourtyard Room
10:30 – 11:00Q&A to Vladimir’s talks RNAseq part I and IICourtyard Room
11:00 – 11:30Coffee break
11:30 – 12:30Q&A to Raffaele’s talk RNAseq: Reads to genesCourtyard Room
12:30 – 14:00Lunch
14:00 – 16:00Practical: From Reads to Genes (Bulk and single cell)
Raffaele Calogero – University of Torino, Italy
Courtyard Room
16:00 – 16:30Coffee break
16:30 – 18:00Q&A on RNAseq and scRNAseqCourtyard Room
18:00 – 18:20Packing and cleaning of work stationsCourtyard Room
18:20 Shuttle to ISG Hotel ATC entrance
18:45DinnerISG Hotel
Day 2 – Monday 7 March 2022
Time SpeakerLocation
09:30 – 10:30Flash talk presentationsCourtyard Room
10:30 – 12:30Practical & theory: Differential expression analysis.
Raffaele Calogero – University of Torino, Italy
with flexible coffee break
Courtyard Room
12:30 – 14:00Lunch
14:00 – 16:00Practical session: Ribosome profiling
Gerben Menschaert – University of Ghent, Belgium
Courtyard Room
16:00 – 16:30Coffee break
16:30 – 18:30Lecture/practicals: Ribosome profiling
Gerben Menschaert – University of Ghent, Belgium
Courtyard Room
18:30 – 18:50Packing and cleaning of work stationsCourtyard Room
18:50 – 19:50Dinner
20:00 Shuttle to ISG Hotel ATC entrance
Day 3 – Tuesday 8 March 2022
Time SpeakerLocation
9:30 – 11:00Introduction to Proteomics, Jeroen KrijgsveldCourtyard Room
11:00 – 11:30Coffee break
11:30 – 12:30Lecture: Quantitative proteomics: SILAC and other MS1-based approaches
Jeroen Krijgsveld – DKFZ, Germany
Courtyard Room
12:30 – 14:00Lunch
14:00 – 15:00Lecture: Quantitative proteomics: TMT
Mikhail Savitski – EMBL Heidelberg, Germany
Courtyard Room
15:00 – 16:00Lecture: Bioinformatics for proteomics
Lennart Martens – University of Ghent, Belgium
Courtyard Room
16:00 – 16:30Coffee Break
16:30 – 17:30Q&A to Bioinformatics for proteomics
Lennart Martens – University of Ghent, Belgium
Courtyard Room
17:30 – 17:50Packing and cleaning of work stationsCourtyard Room
18:00 – 19:00Dinner
19:20Shuttle to ISG HotelATC entrance
Day 4 – Wednesday 9 March 2022
Time SpeakerLocation
09:30 – 10:00Practical Session: Turning data into information-peptide and protein identification, database searching
Lennart Martens – University of Ghent, Belgium
with flexible coffee break
Courtyard Room
10:00 – 12:00Lecture: Introduction to MaxQuant; analysis of MS data
Daria Fijalkowska – University of Ghent, Belgium
Courtyard Room
12:00 – 13:30Lunch
13:30 – 14:00Practical Session: Proteomics data interpretation
Daria Fijalkowska – DKFZ, Germany
Courtyard Room
14:30 – 16:30Lecture: P-values and multiple testing correction
Hyungwon Choi – National University of Singapore, Singapore
Courtyard Room
16:30 – 17:30Coffee Break
17:30 – 17:50Packing and cleaning of work stationsCourtyard Room
18:00Shuttle to ISG Hotel
18:00Dinner
Day 5 – Thursday 10 March 2022
Time SpeakerLocation
09:30 – 10:00Q&A to Bioinformatic tools for data comparison and integration
John “Scooter” Morris – University of California, San Francisco
Courtyard Room
10:00 – 12:30Practical: Introduction to Cytoscape
Manjeet Kumar – EMBL Heidelberg, Germany
John “Scooter” Morris – University of California, San Francisco, USA
with flexible coffee break
Courtyard Room
12:30 – 14:00Lunch
14:00 – 16:00Practical: Introduction to Cytoscape
Manjeet Kumar – EMBL Heidelberg, Germany
John “Scooter” Morris – University of California, San Francisco, USA
Courtyard Room
16:00 – 16:30Coffee Break
16:30 – 17:30Lecture and Practical: Enrichment analysis
Manjeet Kumar – EMBL Heidelberg, Germany
John “Scooter” Morris – University of California, San Francisco, USA
Courtyard Room
17:30 – 17:50Packing and cleaning of work stationsCourtyard Room
18:00Shuttle to ISG HotelATC entrance
18:30Dinner
Day 6 – Friday 11 March 2022
TimeSpeakerLocation
9:30-10:30Application talk: Network-oriented integrative multi-omics analysis of tissues and fluids – case studies in cancer and cardiovascular diseases
Hyungwon Choi – National University of Singapore, Singapore
with flexible coffee break
Courtyard Room
10:30-13:00Practical Session: Data integration
John “Scooter” Morris – University of California, San Francisco, USA
Courtyard Room
13:00-14:30Lunch
14:30-17:00Practical Session: Data integration
John “Scooter” Morris – University of California, San Francisco, USA
with flexible coffee break
Courtyard Room
17:00-17:30Course wrap-up and farewellCourtyard Room
17:30 Bus to Heidelberg train station and city center 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.

Participants are expected to book and pay their own accommodation and travel expenses. 

Academia€690
PhD Student€690
Industry€1150

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 more detailed information, follow the instructions provided in 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 events in Heidelberg and will be indicated during the abstract or motivation letter submission process.

Your place in the meeting 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 or conference.

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, EMBL Conference or EMBO|EMBL Symposium from within Europe.
– up to €1000 for participants travelling to an EMBL Course, EMBL Conference or EMBO|EMBL Symposium from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

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.

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 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.

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

See our list of external funding opportunities and information on attending a conference as an event reporter.

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

Accommodation and Shuttles

Single rooms have been reserved for 6 nights (5 – 11 March 2022) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code PRO22-01). 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

Technical Requirements

Below you will find the software and technical requirements for this course.

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

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.

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: 6 - 11 Mar 2022

Location: EMBL Heidelberg


Deadline(s):

Application: Closed


Organisers:

  • Vladimir Benes
    EMBL Heidelberg, Germany
    • Raffaele Calogero
      University of Turin, Italy

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

Founder partners

Corporate partners

Associate partners

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