E-GEOD-8425 - Transcription profiling of mouse laser dissected hippocampus of Rasgrf1 knockout mice

Submitted on 10 July 2007, released on 16 June 2008, last updated on 2 May 2014
Mus musculus
Samples (6)
Array (1)
Protocols (5)
We used manual macrodissection or laser capture microdissection (LCM) to isolate tissue sections of the hippocampus area of Ras-GRF1 wild type and knockout mice brains, and analyzed their transcriptional patterns using commercial oligonucleotide microarrays. Comparison between the transcriptomes of macrodissected and microdissected samples showed that the LCM samples allowed detection of significantly higher numbers of differentially expressed genes, with higher statistical rates of significance. These results validate LCM as a reliable technique for in vivo genomic studies in the brain hippocampus, where contamination by surrounding areas (not expressing Ras-GRF1) increases background noise and impairs identification of differentially expressed genes. Comparison between wild type and knockout LCM hippocampus samples revealed that Ras-GRF1 elimination caused significant gene expression changes, mostly affecting signal transduction and related neural processes. The list of 36 most differentially expressed genes included loci concerned mainly with Ras/G protein signaling and cytoskeletal organization (i.e. 14-3-3γ/ζ, Kcnj6, Clasp2) or related, cross-talking pathways (i.e. jag2, decorin, strap). Consistent with the phenotypes shown by Ras-GRF1 knockout mice, many of these differentially expressed genes play functional roles in processes such as sensory development and function (i.e. Sptlc1, antiquitin, jag2) and/or neurological development/neurodegeneration processes affecting memory and learning. Indeed, potential links to neurodegenerative diseases such as Alzheimer disease (AD) or Creutzfeldt-Jacobs disease (CJD), have been reported for a number of differentially expressed genes identified in this study (Ptma, Aebp2,Clasp2, Hebp1, 14-3-3γ/ζ, Csnk1δ, etc.). These data, together with the previously described role of IRS and insulin (known Ras-GRF1 activators) in AD, warrant further investigation of a potential functional link of Ras-GRF1 to neurodegenerative processes. Experiment Overall Design: 6 samples of tissue sections of the hippocampus area of wild type (WT) and Rasgrf1 knockout (KO) mice brains, 3 biological replicates of each.
Experiment types
transcription profiling by array, unknown experiment type
Investigation descriptionE-GEOD-8425.idf.txt
Sample and data relationshipE-GEOD-8425.sdrf.txt
Raw data (1)E-GEOD-8425.raw.1.zip
Processed data (1)E-GEOD-8425.processed.1.zip
Array designA-AFFY-36.adf.txt
R ExpressionSetE-GEOD-8425.eSet.r