1. Gene Expression Omnibus (GEO)

2. Microarrays in gene expression
A typical gene expression analysis experiment:
Differential systems – e.g. cancer vs. normal, drug vs. no drug
Choose/prepare the microarray
Extract total mRNA (transcriptome)
Reverse transcription/dye labeling
Combine equal amounts
Hybridize
Scan
ANALYSE AND INTERPRET THE RESULTS – this is the tricky part…

3. Microarrays in gene expression

4. SPOTS

5. Hybridization

6. SCAN

7. Gene Expression Omnibus (GEO): Gene Expression and Molecular Abundance Data Repository
A public repository for the archiving and distribution of gene expression data submitted by the scientific community.
Curated, online resource for gene expression data browsing, query, analysis and retrieval.
Convenient for deposition of gene expression data, as required by funding agencies and journals.

8. GEO Architecture GEO has four kinds of data records
Platform (GPL) = the technology used and the features detected.
Sample (GSM) = preparation and description of the sample.
Series (GSE) defines a set of samples and how they are related.
DataSets (GDS) sample data collections assembled by GEO staff.

9. GEO Architecture GPL GSM GSE GDS Submitted by Experimentalists
Manufacturer
Curated by
NCBI
GPL
Platform
descriptions
GSM
Raw/processed
spot intensities
from a single
slide/chip
GSE
Grouping of
slide/chip data
“a single experiment”
GDS
Grouping of
experiments

10. GEO Home Page Simple interface to: show status find documentation
query data
browse data

11. Platform Accession Page
Platform details:
Description
Type
Organism
Manufacturer
Related samples and series
NOTE THE TOP BAR (SCOPE)

12. Sample Accession Page Sample details: Description Type Organism Source
Related platforms and series

13. Sample File Data Table Data table field descriptions
Truncated data table from Quick view
Total data rows and file size

14. Series Accession Page Biological sample summary Design summary
Publication information
Related platforms and samples

15. DATASET or GENE PROFILE search
GEO data can be queried as:
Datasets: experiment-centric view using Entrez GEO DataSets
Gene profiles: gene-centric view using Entrez GEO Profiles
Selecting either takes you to a similar Entrez introduction page

16. Querying GEO DataSets
Start a GEO DataSets search with the Query>DataSets text box
This brings up an Entrez GEO DataSets results form

17. DataSet Search Results

18. GEO DataSet Record

19. GENE PROFILE search

20. GEO Gene Profiles

21. GEO Gene Profiles

22. Querying GEO with IDs from Papers
A common way to access GEO data is through accessions from papers.
Online journals include hyperlinks to the GEO accession page.
Or, at the GEO home page enter the accession into the Query>GEO accession text box

23. GEO Links in PubMed Search Results
One option for displaying PubMed search results is GEO DataSet links.
When present, the results page is actually from Entrez GEO DataSets.

24. GEO BLAST