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E-GEOD-6708 - Transcription profiling of monkey thalamus

Status
Submitted on 10 January 2007, released on 15 June 2008, last updated on 27 March 2012
Organism
Macaca mulatta
Samples (10)
Array (1)
Protocols (4)
Description
Nuclei of the mammalian thalamus are aggregations of neurons with unique architectures and input-output connections, yet the molecular determinants of their organizational specificity remain unknown. By comparing expression profiles of thalamus and cerebral cortex in adult rhesus monkeys we identified transcripts that are unique to dorsal thalamus or to individual nuclei within it. Real-time quantitative polymerase chain reaction and in situ hybridization analyses confirmed the findings. Expression profiling of individual nuclei microdissected from the dorsal thalamus revealed additional subsets of nucleus-specific genes. Functional annotation using Gene Ontology (GO) vocabulary and Ingenuity Pathway analysis revealed over-representation of GO categories related to development, morphogenesis, cell-cell interactions, and extracellular matrix within the thalamus- and nucleus-specific genes-many involved in the Wnt signaling pathway. Examples included the transcription factor TCF7L2, localized exclusively to excitatory neurons, a calmodulin-binding protein PCP4, the bone extracellular matrix molecules SPP1 and SPARC, and other genes involved in axon outgrowth and cell matrix interactions. Other nucleus-specific genes such as CBLN1 are involved in synaptogenesis. The genes identified likely underlie nuclear specification, cell phenotype and connectivity during development and their maintenance in the adult thalamus. Experiment Overall Design: To determine the molecular underpinnings of nuclear specificity in the dorsal thalamus we isolated micro-punches of tissue from nucleus-specific regions and processed them for microarray analysis. Replicate samples from 5 separate dorsal thalamic nuclei were processed and compared to identify genes unique to each region. Affymetrix U133A Gene Chips were used. All of the samples were isolated from untreated adult monkey brain.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Nucleus- and cell-specific gene expression in monkey thalamus. Karl D Murray, Prabhakara V Choudary, Edward G Jones. Proc Natl Acad Sci U S A 104(6):1989-94 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-6708.idf.txt
Sample and data relationshipE-GEOD-6708.sdrf.txt
Raw data (1)E-GEOD-6708.raw.1.zip
Processed data (1)E-GEOD-6708.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-6708.eSet.r
Links