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Series GSE5035 Query DataSets for GSE5035
Status Public on Jun 09, 2006
Title zhang-affy-arabi-50806
Organism Mus musculus
Experiment type Expression profiling by array
Summary In our original grant we proposed to use the NR3B-null mouse model to study the role of NR3B subunit in motor neuron function. We have now successfully generated NR3B null mice. Interestingly, NR3B-null mice invariably die at age P4-P8. Our preliminary examination indicates that the motor strength of these mice is severely impaired prior to death. As we continue to explore the cause of death in NR3B null mice, we propose to conduct gene profiling experiments to search for transcription changes in the brain related to ablation of the NR3B gene. We would like to use the facility provided by the NINDS/NIMH Microarray Consortium to identify true outlier genes that show abnormal expression patterns in these mice. Analysis of these outlier genes will help to identify changes in networks and pathways that may cause the death of NR3B-null mice. These studies will further help to elucidate the functional role of NR3B in motor neurons.
We will compare samples from the hindbrain and spinal cord of wild type and NR3B null mice to identify true outlier genes that show abnormal expression patterns, which may be implicated in the death of NR3B-null mice
We hypothesize that genes with their transcription level changing significantly by ablation of NR3B will be associated with the molecular mechanism underlying the death of motor neurons in NR3B null mice.
As NR3B is expressed primarily in the hindbrain and spinal cord, we will first collect and analyze the hindbrain and spinal cord samples from NR3B null mice and wild-type controls in triplicate at two time points (P0 and P5). Total RNA from total 12 samples will be purified. Extracted RNAs will be treated for with DNase I to remove contaminating genomic DNA. The purified RNA will be sent to the NINDS/NIMH Microarray Consortium to generate biotin-labeled probe according to the Affymetrix protocol. These probes will be used to hybridize the GeneChip Mouse Genome 430 2.0 Array. The hybridization, scanning, and initial data analysis of these GeneChips will be conducted by the Consortium staff. We will analyze the collected data further after data collection. We will use computer software, GeneSpring (Silicon Genetics, Redwood City, CA), to analyze data from microarray experiments. We will first identify genes that show significant changes between wild-type and NR3B null mice by applying ANOVA analysis to sample groups of different ages. The genes identified in this manner will then be subjected to hierarchical (Gene tree) and nonhierarchical (K-means) cluster analysis, in order to group them according to similar expression patterns. Another clustering method, the self-organizing map, will be used to determine whether one gene cluster is a variant of another. Finally, the Principal Components Analysis (PCA) will be employed to analyze large sample groups, which may include experimental variability with respect to age, anatomical location and genotype. We will determine from these analysis whether further experiments are needed using different array platforms, such as Agillent Oligo Array.
Keywords: time-course
 
 
Contributor(s) Zhang D
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Submission date Jun 09, 2006
Last update date Feb 11, 2019
Contact name Winnie Liang
E-mail(s) wliang@tgen.org
Organization name Translational Genomics
Street address 445 N. Fifth Street
City Phoenix
State/province AZ
ZIP/Postal code 85012
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (12)
GSM113679 brain, hindbrain and spinal cord: P0WT1_e1_le1
GSM113680 brain, hindbrain and spinal cord: P0WT2_e1_le1
GSM113681 brain, hindbrain and spinal cord: P0WT3_e1_le1
Relations
BioProject PRJNA96665

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Supplementary file Size Download File type/resource
GSE5035_RAW.tar 42.5 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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