E-GEOD-56458 - Endogenous Elevation of Homocysteine Induces Retinal Neuron Death in the Cystathionine-b-Synthase Mutant Mice

Status
Released on 4 April 2014, last updated on 3 June 2014
Organism
Mus musculus
Samples (6)
Array (1)
Protocols (9)
Description
The effects of endogenous elevation of homocysteine on retinal gene expression were screened by microarray analysis, which was performed in triplicate (i.e., three different paired RNA samples) with RNA isolated from neural retinas of cbs+/- HM at 5-weeks after a methionine diet and age-matched wildtype mice. The microarray chips used in this study permitted the screening of 36,212 genes. Of particular interest were those genes in cbs+/- HM mice whose expression levels changed by at least a factor of 2 (increased or decreased expression) compared with the wild-type in each of the replicate experiments. Using these selection criteria, we identified 1219 genes. They were categorized into six functional groups: (1) proapoptosis, (2) antiapoptosis, (3) cell cycle, (4) antioxidant, (5) calcium signaling, and (6) axon growth/guidance, with the remaining genes with marked changes in expression placed in a miscellaneous group. After categorization, relevant genes were further narrowed by SAM analysis; q < 0.06 was considered significant. Microarrays were performed in triplicate as biological repeats and reverse fluoro (i.e., three different paired RNA samples) with RNA isolated from neural retinas of cbs+/- HM at 5-weeks after a methionine diet and age-matched wildtype mice after a methionine diet.
Experiment type
transcription profiling by array 
Contacts
Sylvia Smith <Sbsmith@gru.edu>, Barbara A Mysona, Brent Moister, Jennifer Duplantier, Kebin Liu, Marlena J Farley, Penny Roon, Preethi S Ganapathy, Puttur D Prasad, Sylvia B Smith, Tracy K Moister, Ying Dun
Citation
Endogenous elevation of homocysteine induces retinal neuron death in the cystathionine-beta-synthase mutant mouse. Ganapathy PS, Moister B, Roon P, Mysona BA, Duplantier J, Dun Y, Moister TK, Farley MJ, Prasad PD, Liu K, Smith SB. , Europe PMC 19357353
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-56458.idf.txt
Sample and data relationshipE-GEOD-56458.sdrf.txt
Raw data (1)E-GEOD-56458.raw.1.zip
Processed data (1)E-GEOD-56458.processed.1.zip
Array designA-GEOD-4200.adf.txt
Links