Managing single cell transcriptomics data


 Wednesday 3 Friday 5 July 2019


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Thursday 04 April 2019

Application deadline: 

Friday 14 June 2019


First come, first served


Marina Pujol

Registration fee: 


Registration closed

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This course aims to provide researchers generating and working with single-cell RNA sequencing or image-based transcriptomics data with the tools and knowledge for generating high-quality metadata alongside their data and analyses. Participants will learn what it means to make their data FAIR (Findable, Accessible, Interoperable, and Reusable) and what tools and standards are available to help them with good data management and FAIRification. Finally, participants will learn about the Human Cell Atlas project and how to ensure their data reaches the wider research community.


This course is aimed at researchers who are generating, planning on generating, or working with single cell RNA sequencing or image-based transcriptomics data. This course will not cover any aspects of data analysis, therefore no prior computational knowledge is required.

Syllabus, tools and resources

During this course you will learn about:

  • General principles of data management, data FAIRification and best practice for generating and working with single cell RNA sequencing and image-based transcriptomics data
  • Experimental design for single cell experiments
  • HCA data and metadata standards


After this course, you should be able to:

  • Describe single cell RNA sequencing and image-based transcriptomic technologies and apply appropriate experimental approaches
  • Define best practice for managing cellular resolution data
  • Know which standards for data and metadata need to be applied to data being generated
  • Choose appropriate ontologies for annotation of data
  • Explore the HCA and prepare quality data to be submitted to the Atlas

Additional information

Accommodation will be provided at the Wellcome Genome Campus Conference Centre, Wednesday-Friday.  Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates.

The course includes evening meals at the Hinxton Hall Restaurant on campus, and breaks and lunches outside the EMBL-EBI training rooms.

A bus will take you to Cambridge Train Station at the end of the course. 


Day 1 – Wednesday 3rd July 2019
12:00 – 13:00 Arrival, registration and lunch  
13:00 – 13:30 Welcome to EMBL-EBI and introductions Wendi Bacon
13:30 – 14:00 Participant introductions Wendi Bacon
14:00 – 15:00 What is ‘good data management’ and why do we need it? Wendi Bacon
15:00 – 15:30 Break  
15:30 – 16:00 Data management: Tales from the Lab Bench Wendi Bacon
16:00 – 17:30 FAIRifying your data for publication using ontologies and standards Dani Welter & Mallory Freeberg
17:30 – 18:00 Group discussions Wendi Bacon & Mallory Freeberg
18:00  End of day  
18:15 Check into accommodation  
19:00 Dinner at Hinxton Hall  
Day 2 – Thursday 4th July 2019
9:00 –  9:30  What's a server? Computational terms & other questionable questions Wendi Bacon, Alfonso Fuentes, Brett McClintock 
9:30 – 11:00 Single cell RNA sequencing technology overview Wendi Bacon
11:00 – 11:30 Break  
11:30 – 13:00 Experimental design considerations Lia Chappell & Jenni Westoby
13:00 – 14:00 Lunch  
14:00 – 15:00 Spatially resolved transcriptomics technology overview Zina Perova
15:00 – 15:30 Break  
15:30 – 17:00 Experimental design considerations Zina Perova
17:00 – 17:30 Group discussions Wendi Bacon & Zina Perova
17:30 End of day  
18:30 Dinner at Hinxton Hall  
Day 3 – Friday 5th July 2019
9:00 – 9:30 HCA overview Mallory Freeberg
 9:30 – 10:30 Data and metadata standards for HCA Dani Welter
10:30 – 11:00 Coffee  
11:00 – 12:00 Submission to HCA Mallory Freeberg
12:00 – 12:30 Discussion Mallory Freeberg
12:30 – 13:00 Wrap-up and feedback Mallory Freeberg & Sarah Morgan
13:00 – 13:45 Lunch  
13:45 Bus to Cambridge Train Station