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E-GEOD-20430 - Expression data from Gambian children with and without the clinical signs of active trachoma: HG-focus array

Status
Released on 3 September 2010, last updated on 10 June 2011
Organism
Homo sapiens
Samples (29)
Array (1)
Protocols (8)
Description
Results from 29 samples tested on the Affymetrix HG-focused target array identified transcriptional changes characteristic of ocular disease and ocular Chlamydia trachomatis infection phenotypes. Large numbers of differentially regulated genes were demonstrated. These were characteristic of the host defence response and typical of innate responses at epithelial surfaces and infiltrating leukocytes. These results provide an insight into the complexity of the acute response in trachoma. Samples from 29 participants were tested on the HG-Focus target arrays (17 participants with clinical signs of active trachoma and 12 study participants with normal conjunctivas from the same trachoma endemic population as controls). Conjunctival samples from an additional 60 participants were tested on U133 plus 2.0 arrays and are reported elsewhere. This second set of independent samples was used to assess different gene classifier selection methods and validation tests using >8500 common probe-sets shared between HG-focus target and U133 plus 2.0 arrays. Potential biomarkers of disease and infection are identified.
Experiment type
transcription profiling by array 
Contacts
Martin James Holland <Martin.Holland@lshtm.ac.uk>, Angels Natividad, David C Mabey, David Jeffries, Martin J Holland, Matthew J Burton, Robin L Bailey
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-20430.idf.txt
Sample and data relationshipE-GEOD-20430.sdrf.txt
Raw data (1)E-GEOD-20430.raw.1.zip
Processed data (1)E-GEOD-20430.processed.1.zip
Array designA-AFFY-41.adf.txt
R ExpressionSetE-GEOD-20430.eSet.r
Links