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GEO ~ The NCBI Gene Expression Omnibus

logo for Gene Expression Omnibus linking to website

Deep Sequencing Core Lab users may be interested in using GEO, the NCBI Gene Expression Omnibus. Click on the above GEO graphic to visit the NIH main page. GEO serves as a repository for data from gene expression experiments which is freely available to all members of the scientific community. Researchers performing experiments which generate large amounts  of data (e.g. deep sequencing and microarrays) may deposit their datasets to GEO (even if unpublished). Each dataset is identified by a unique ID number which can be cited in publications; many journals require a GEO ID number now when publishing data generated by high-throughput methods.

GEO accepts sequence data generated by next-generation sequencing methodology (Solexa, now Illumina). The following three components should be zipped or tarred together and transferred directly to GEO by selecting the 'GEOarchive' option on the direct deposit page ( Click Here for Deposit Page ).

Component 1: Metadata spreadsheet
Descriptive information and protocols for the overall experiment and individual samples.

Component 2: The processed data files
Plain text, tab-delimited table that contains filtered, unique sequence reads,
detection counts and sequence mapping information

Component 3: The raw data files
_seq.txt
_prb.txt
_sig2.txt
_qhg.txt

For detailed instruction, please refer to
http://www.ncbi.nlm.nih.gov/geo/info/seq.html
or email to geo@ncbi.nlm.nih.gov


Some useful references
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The GEO projects page
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http://www.ncbi.nlm.nih.gov/projects/geo

Please send your comments, suggestions, and user notes to share with
other core lab users to NEMO@umassmed.edu

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