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Series GSE39372 Query DataSets for GSE39372
Status Public on Jul 17, 2012
Title Proteogenomics of synaptosomal mitochondrial oxidative stress
Organism Mus musculus
Experiment type Expression profiling by array
Summary There has been increasing interest in the quantification and characterization of messages and proteins at the synapse, due to its importance in neurodegenerative disease, most notably Alzheimer’s disease. Here, we report the transcriptomic and proteomic changes that occur in synaptosomes from frontal cortices of Sod2 null mice. Constitutively null Sod2 mice were differentially dosed with the synthetic catalytic antioxidant EUK-189, which can extend the lifespan of these mice, as well as uncover or prevent neurodegeneration due to endogenous oxidative stress. This approach facilitated insight into quantification of trafficked messages and proteins to the synaptosome. We used two complementary methods to investigate the nature of the synaptosome under oxidative stress; either whole genome gene expression microarrays or mass spectrometry-based proteomics using isobaric tagging for relative and absolute quantitation (iTRAQ) of proteins. We have characterized the relative enrichments of gene ontologies at both gene and protein expression that occur due to mitochondrial oxidative stress in the synaptosome, which may lead to new avenues of investigation in understanding the regulation of the synaptic function in normal and diseased states. As a result of using these approaches, we report for the first time an activation of the mTOR pathway in synaptosomes isolated from Sod2 null mice, confirmed by an upregulation of the phosphorylation of 4E-BP1.
 
Overall design mRNA was extracted from synaptosome samples of individual mice from each genotype/treatment group (N=9-11 per group/treatment). 200ng of the purified total RNA was then amplified one round using Ambion’s Illumina RNA Amplification Kit, to prepare cRNA for labeling and hybridization to Illumina’s MouseRef-8 v2.0 expression bead chips as per the manufacturers instructions (Illumina, San Diego, CA, USA).
 
Contributor(s) Flynn JM, Czerwieniec GA, Choi SW, Day NU, Gibson BW, Hubbard A, Melov S
Citation(s) 22796328
Submission date Jul 16, 2012
Last update date Jun 14, 2018
Contact name Simon Melov
Organization name Buck Institute for Research on Aging
Lab Melov Lab
Street address 8001 Redwood Blvd
City Novato
State/province CA
ZIP/Postal code 94945
Country USA
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (50)
GSM966947 Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out HKO-1
GSM966948 Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out HKO-2
GSM966949 Synaptosomal RNA from High Dose treated (EUK8) Constitutive Sod2 knock out HKO-3
Relations
BioProject PRJNA170733

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39372_RAW.tar 3.1 Mb (http)(custom) TAR
GSE39372_non-normalized.txt.gz 5.9 Mb (ftp)(http) TXT
Processed data included within Sample table
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