| Citing the GEO database |
Edgar R, Domrachev M, Lash AE.
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Nucleic
Acids Res. 2002 Jan 1;30(1):207-10
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R.
NCBI GEO: mining tens of millions of expression profiles--database and tools update
Nucleic Acids Res. 2006 Nov 11
More GEO publications here.
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| Citing your GEO submission |
"The data discussed in this publication have been deposited in NCBI's Gene
Expression Omnibus (Edgar et al., 2002) and are
accessible through GEO Series accession number GSExxx (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSExxx)."
We strongly recommend that submitters cite their Series accession number (GSExxx) because that record summarizes the experiment and includes links to all other
relevant data.
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| Citing data you find in GEO |
In addition to citing one of the GEO database papers listed above for general use of GEO, if applicable,
you should cite the original paper and the accession number used to identify the experiment(s) in GEO.
That way the original generators of the data sets will get credit and allow readers to locate the source.
The original paper (if available) is listed under the 'Citation' section of the Series and DataSet records.
Example: "Smith et al., 2006, recently performed microarray experiments investigating effect of compound X on neurons (data accessible at NCBI GEO database (Edgar et al., 2002), accession GSExxx)."
Example: "In March 2008, a search of the GEO Profiles database (Barrett et al., 2006) revealed that Gene X is upregulated in response to compound Y (GEO accession GDSxxx; Smith et al., 2006)."
Also, please see Disclaimer.
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| Linking to GEO accessions |
A specific GEO Platform (GPLxxx), Sample (GSMxxx), or Series (GSExxx)
record may be linked as follows:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSExxx
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPLxxx
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSMxxx
where xxx is the numerical part of the accession.
We recommend linking to the Series object because it summarizes the experiment and includes links to all other
relevant accessions.
Example: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6364 |
| Linking to GEO DataSet records |
A specific DataSet (GDSxxx) record may be linked as follows:
http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi?gds=xxx
where xxx is the numerical part of the accession.
Example: http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi?gds=2737
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| Linking to Entrez GEO Profiles |
Specific profile(s) can be linked using a query term as follows:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term="query term"
Example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term=GDS621+AND+L13606_at
Example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo&term=dab2[gene+symbol]+AND+human[organism]+AND+dystrophy
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| Linking to Entrez GEO DataSets |
Specific DataSet(s) can be linked using a query term as follows:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term="query term"
Example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=GDS181+AND+gds[entry+type]
Example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds&term=Saccharomyces+cerevisiae[organism]+AND+stress
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