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)
3.
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)
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
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
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)