From microarrays to RNA-seq. From archiving experiments to Gene Expression Atlas.

1. From microarrays to RNAseq
From archiving experiments to Gene
Expression Atlas
Alvis Brazma
European Bioinformatics Institute

2. European Bioinformatics Institute (EBI)
• EBI is in Hinxton, ~10 miles South of Cambridge, UK
Wellcome Trust Genome Campus
• EBI is part of EMBL, ~like CERN for molecular biology
• ~500 scientific and IT staff at EBI
• Hosting the ELIXIR node (details to follow)

4. Building an archive of public gene expression
data (www.ebi.ac.uk/arrayexpress)

5. Building an archive of public gene expression
data (www.ebi.ac.uk/arrayexpress)

6. Search for cancer

8. 150 citations of ArrayExpress publications
using the data in 2011:

9. From microarrays to RNAseq
ArrayExpress9

10. NGS vs Array data in ArrayExpress
1
10
100
1000
10000
2009 2010 2011 2012
Array data
Sequencing data

13. Experiment details

14. MINSEQE - Minimum Information about a
high-throughput SeQuencing Experiment
1. The description of the biological system and the
particular states that are studied
2. The sequence read data for each assay
3. The 'final' processed (or summary) data for the set of
assays in the study
4. The experiment design including sample data
relationships
5. General information about the experiment
6. Essential experimental and data processing protocols

16. ArrayExpress
ArrayExpress
Archive
Primary DB
Expression
Atlas
Added Value DB
Curation
EFO annotation
statistical computationsSubmissions
and
GEO import
curation
Users –
bioinformaticians
Users –
all biologists

17. Query for genes
Query for conditions
Mission - making ArrayExpress data
accessible to every biologist
Igfbp4

18. Experiment view

19. Baseline Expression
e.g. which genes are
expressed in a normal
human kidney?
Differential Expression
e.g. which genes are up-
regulated in pancreatic islets
of pregnant mice?
www-test.ebi.ac.uk/gxa

20. www-test.ebi.ac.uk/gxa
Baseline Expression
quality control
pain%ng
by
shardcore
(h2p://www.shardcore.org/)
low-quality reads
NNACGANNNNN
mapping
Baseline
quantification
summarization
RNA-seq Processing Pipeline

21. www-test.ebi.ac.uk/gxa
Baseline Expression
Experimental Factors:
• Tissue
• RNA type
• Cellular component
• Cell lineExperiments so far (RNA-seq):
• Illumina Body Map (16 runs)
• Transcriptome of DBAxC57BL/6J mice (36 runs)
• RNA-seq of long coding and long non coding RNAs from ENCODE cell lines (162 runs)
• RNA-seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in
mammalian organs (127 runs)

22. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

23. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

24. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

25. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

26. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

27. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

28. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
*Rando, T. A. Nature 441, 1080-1086 (29 June 2006) | doi:10.1038/nature04958
Stem cells, ageing and
the quest for immortality

29. www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)

30. www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Inclusion of Proteomics Data

31. www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Genome Browser View

32. www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Comparable Experiments
Now Future

33. Future Plans – Atlas Home Page
www-test.ebi.ac.uk/gxa
We need your feedback!

34. Robert Petryszak

35. Funding
• EMBL member countries
• European Commission FP7 grants

36. Questions
www-test.ebi.ac.uk/gxa