Transcript GEO - TeachLine

Gene Expression Omnibus (GEO)
http://www.ncbi.nlm.nih.gov/geo/
Microarrays in gene expression

A typical gene expression analysis experiment:
1.
2.
3.
4.
5.
6.
7.
8.
Differential systems – e.g. cancer vs. normal, drug vs. no
drug
Choose/prepare the microarray
Extract total mRNA (transcriptome)
Reverse transcription/dye labelling
Combine equal amounts
Hybridize
Scan
ANALYSE AND INTERPRET THE RESULTS – this is
the tricky part…
Microarrays in gene expression
SPOTS
Hybridization
SCAN
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.
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.
GEO Architecture
Submitted by
Manufacturer
GPL
Platform
descriptions
Submitted by
Experimentalists
GSM
GSE
Grouping of
Raw/processed
slide/chip data
spot intensities
from a single “a single experiment”
slide/chip
Curated by
NCBI
GDS
Grouping of
experiments
GEO Home Page
Simple interface to:
 show status
 find documentation
 query data
 browse data
Platform Accession Page
•Platform details:
•Description
•Type
•Organism
•Manufacturer
•Related samples and
series
NOTE THE TOP BAR (SCOPE)
Sample Accession Page
•Sample details:
•Description
•Type
•Organism
•Source
•Related
platforms and
series
Sample File Data Table
Data table field
descriptions
Truncated data table
from Quick view
Total data rows and
file size
Supplementary raw
data file
Series Accession Page
•Biological sample summary
•Design summary
•Publication information
•Related platforms and
samples
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
Querying GEO DataSets


Start a GEO DataSets search with the Query>DataSets text box
This brings up an Entrez GEO DataSets results form
DataSet Search Results
GEO DataSet Record
GEO Gene Profiles
GEO Gene Profiles
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
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.
GEO BLAST