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Fri 17 May 2019
09:30 - 17:15

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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EMBL-EBI: Transcriptomics Data and Tools
BeginnersPrerequisites

Fri 17 May 2019

Description

This workshop is designed for researchers interested in learning about functional genomics data, how to access, retrieve and use the data from ArrayExpress and hands-on experience in using Expression Atlas, a resource to find information about gene and protein expression across species and biological conditions such as different tissues, cell types, developmental stages and diseases among others. This will include an overview on how gene expression data is curated and analysed in Expression Atlas and a practical activity to demonstrate how to access and visualise gene expression analysis results. These activities should help you answer questions such as "where is my favourite gene expressed?" or "how does its expression change in a disease?".

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • The module is suitable for researchers interested in gene expression analysis and visualisation
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites

No previous bioinformatics experience is required, but an undergraduate level understanding of biology would be an advantage

Sessions

Number of sessions: 1

# Date Time Venue Trainers
1 Fri 17 May   09:30 - 17:15 09:30 - 17:15 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Nancy George,  Silvie Fexova
Topics covered

Bioinformatics, Database search, Data retrieval, Transcriptomics, Gene expression

Objectives

After this course you should be able to:

  • browse and retrieve functional genomics data from ArrayExpress with ease
  • search and extract functional genomics data effectively with specific filter
  • describe the caveats and limitations behind the searches made against the ArrayExpress database
  • find information on the abundance and localisation of RNA (and proteins) in different species and biological conditions
  • interpret gene expression analysis results through heatmap visualisation
Aims

During this course you will learn about:

Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics
9:30 - 9:45 Welcome and introduction to EMBL-EBI resources and tools
9:45 - 10:45 Data quality: standards and ontologies
10:45 - 11:00 Tea/ Coffee break
11:00 - 12:00 Discover functional genomics data with ArrayExpress
12:00 - 13:00 Lunch (not provided)
13:00 - 14:00 Discover functional genomics data with ArrayExpress: Practical session
14:00 - 15:00 Explore gene expression data with Expression Atlas
15:00 - 15:30 Tea/ Coffee break
15:30 - 16:30 Explore gene expression data with Expression Atlas: Practical session
16:30 - 17:15 Single Cell Expression Atlas: a new tool for single cell transcriptomics
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

1

Frequency

A number of times per year

Related

Related courses
Theme
Databases and Services

Booking / availability