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

EMBL Course

Analysis and integration of transcriptome and proteome data

Overview

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

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.

What past participants say about the course

“This course organised by EMBL is an excellent opportunity for wet lab biologists to gain skills and understand the necessary bioinformatic background for both designing experiments and performing data analysis.” – Katarzyna Tutak, Institute of Human Genetics, Polish Academy of Science

Speakers

Speakers, trainers, and staff

Scientific organisers

Course organisers

Maria Mercedes Bacadare Goitia

Course and Conference Manager

EMBL Heidelberg

Germany

Programme

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  • 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.

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

Day 1 – Sunday 26 February 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00 – 09:15Arrival, welcome and safety introductionsCourtyard room
09:15 – 11:00RNA-seq: cool but is it that simple?
Vladimir Benes – EMBL Heidelberg, Germany
Courtyard room
11:00 – 11:30Coffee breakATC Foyer
11:30 – 12:30RNAseq: Reads to genes
Jonathan Landry – EMBL Heidelberg, Germany
Jan Provaznik – EMBL Hiedleberg, Germany
Kristina Roucova – Univerzita Karlova, Czech Republic
Courtyard room
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Practical: From Reads to Genes (Bulk and single cell)
Jonathan Landry – EMBL Heidelberg, Germany
Jan Provaznik – EMBL Hiedleberg, Germany
Kristina Roucova – Univerzita Karlova, Czech Republic
Computer Training Lab
16:00 – 16:30Coffee breakComputer Training Lab
16:30 – 18:00Q&A on RNAseq and scRNAseqComputer Training Lab
18:00Departure to ISG HotelATC entrance
18:30DinnerISG Hotel
Day 2 – Monday 27 February 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00 – 10:00Flash talk presentationsComputer Training Lab
10:00 – 12:30Practical & theory: Differential expression analysis.
Jonathan Landry – EMBL Heidelberg, Germany
Jan Provaznik – EMBL Hiedleberg, Germany
Kristina Roucova – Univerzita Karlova, Czech Republic
with flexible coffee break
Computer Training Lab
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Practical session: Ribosome profiling
Gerben Menschaert – University of Ghent, Belgium
Computer Training Lab
16:00 – 16:30Coffee breakComputer Training Lab
16:30 – 18:30Lecture/practicals: Ribosome profiling
Gerben Menschaert – University of Ghent, Belgium
Computer Training Lab
18:30 – 19:40DinnerEMBL Canteen
19:40Departure to ISG HotelATC entrance
Day 3 – Tuesday 28 February 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00- 11:00Introduction to Proteomics
Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany
Computer Training Lab
11:00 – 11:30Coffee breakComputer Training Lab
11:30 – 12:30Lecture: Quantitative proteomics: TMT
Mikhail Savitski – EMBL Heidelberg, Germany
Computer Training Lab
12:30 – 13:30LunchEMBL Canteen
13:30 – 15:00Lecture: Bioinformatics for proteomics
Lennart Martens – University of Ghent, Belgium
Computer Training Lab
15:00 – 16:00Practical Session: Turning data into information-peptide and protein identification, database searching
Lennart Martens – University of Ghent, Belgium
Computer Training Lab
16:00 – 16:30Coffee BreakComputer Training Lab
16:30 – 18:00Q&A to Bioinformatics for proteomics
Lennart Martens – University of Ghent, Belgium
Computer Training Lab
18:00 – 19:00DinnerEMBL Canteen
19:00Departure to ISG HotelATC entrance
Day 4 – Wednesday 1 March 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00 – 10:00Lecture: Quantitative proteomics: SILAC and other MS1-based approaches
Jeroen Krijgsveld – German Cancer Research Centre (DKFZ), Germany
Computer Training Lab
10:00 – 10:30Coffee break
10:30 – 12:00Lecture: Introduction to MaxQuant; analysis of MS data
Daria Fijalkowska – University of Ghent, Belgium
Computer Training Lab
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:30Practical Session: Proteomics data interpretation
Daria Fijalkowska – University of Ghent, Belgium
Computer Training Lab
14:30 – 16:15Lecture: P-values and multiple testing correction
Hyungwon Choi – National University of Singapore, Singapore
Computer Training Lab
16:15 Free afternoon
16:15Departure to ISG Hotel and downtown
Day 5 – Thursday 2 March 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00 – 10:00Q&A to Bioinformatic tools for data comparison and integration
John “Scooter” Morris – University of California, San Francisco, USA
Computer Training Lab
10:00 – 10:30Coffee break
10:30 – 12:30Practical: Introduction to Cytoscape
John “Scooter” Morris – University of California, San Francisco, USA
Manjeet Kumar – EMBL Heidelberg, Germany
Santhust – EMBL Heidelberg, Germany
Computer Training Lab
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Practical: Introduction to Cytoscape
John “Scooter” Morris – University of California, San Francisco, USA
Manjeet Kumar – EMBL Heidelberg, Germany
Santhust – EMBL Heidelberg, Germany
Computer Training Lab
16:00 – 16:30Coffee breakComputer Training Lab
16:30 – 17:45Lecture and Practical: Enrichment analysis
John “Scooter” Morris – University of California, San Francisco, USA
Manjeet Kumar – EMBL Heidelberg, Germany
Santhust – EMBL Heidelberg, Germany
Computer Training Lab
17:45Departure to ISG Hotel and downtownATC entrance
18:30Downtown Dinner
Day 6 – Friday 3 March 2023
Time (Europe/Berlin)SpeakerLocation
08:40 – 09:00Bus from ISG Hotel to EMBL ATC entranceISG Hotel bus stop
09:00 – 10:00Application 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
Computer Training Lab
10:00 – 10:30Coffee break
10:00 – 12:30Practical Session: Data integration
John “Scooter” Morris – University of California, San Francisco, USA
Computer Training Lab
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Practical Session: Data integration
John “Scooter” Morris – University of California, San Francisco, USA
Manjeet Kumar – EMBL Heidelberg, Germany
Santhust – EMBL Heidelberg, Germany
with flexible coffee break
Computer Training Lab
16:00 – 16:30Course wrap-up and farewellComputer Training Lab
16:30Departure to Train Station and DowntownATC entrance

Practical information

Registration fees and motivation letter

The course is limited to 24 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€1200

NO visa support letters will be issued until payment of the registration fee is confirmed.

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 6 nights (25 Feb – 3 March 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code PRO23-01). 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.

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

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.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

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: 26 Feb - 3 Mar 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: Closed


Organisers:

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

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