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View Project hofma-affy-mouse-370000
Project Summary
Status: Public  
Publications: 1 Published
 		 
Project Detail Data Detail
Platform: Affymetrix MIAME Areas Compliance
Species: Mouse Array Design Detail true
Organ/Tissue Type: brain Experiment Detail true
Organ Region: cochlea Sample Detail false
Cell Type: mixed cell types Hybridization Detail false
Study Type: subclassification Measurement Detail false
Disease/Condition: Neurodegeneration
Replicates: 3
Expected Samples:  
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Available Actions
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Investigator Contact Detail
Name Dr. Sandra L Hofmann
Institution: University of Texas Southwestern Medical Center at Dallas
Street Address: 5323 Harry Hines Boulevard
Mail Code 8593
City, State/Province: Dallas , TX
Zip/Postal Code: 75390-8593
Country: United States
Work Phone: 214-648-4911
Fax: 214-648-4940
E-mail: sandra.hofmann@utsouthwestern.edu
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Proposal Detail
Grant: NS036867
Status: Public
Service Type: Start to Finish Profiling
IACUC: 0433-05-08-2
IACUC date: 2005-07-08
Study Relevance:
Infantile neuronal ceroid lipofuscinosis (aka infantile Batten disease) is a severe neurodegenerative disorder of early childhood characterized by cortical atrophy, blindness and seizures, leading to premature death in the first decade. The disorder is caused by deficiency in a soluble lysosomal enzyme, palmitoyl protein thioesterase-1 (PPT1). PPT1 knockout mice faithfully reproduce the features of the human disease, with motor deterioration, blindness, seizures, and death before 10 months of age. The progression of events leading from enzyme deficiency to organ failure is poorly defined. The neuronal ceroid lipofuscinoses are of particular interest because of the similarities between the accumulated material and lipofuscin that is associated with normal aging.
Hypothesis:
Gene expression profiling of brain tissue from PPT1 knockout mice as compared to normal controls will provide insights into the mechanism of neurodegeneration. Comparison of this profile with gene expression profiles associated with normal aging may provide insights into the contribution of lipofuscin to aging and neurodegeneration.
Specific Aim:
We will determine changes in gene expression that occur during the course of neurodegeneration in PPT1 knockout as compared to control mice.
Experimental Procedure and Design:
PPT1 knockout mice on a C57BL/6 background will be sacrificed under CO2 and whole brains removed and frozen under liquid nitrogen. Three mice will be used for each time point. Data points will be collected at 3 months, 5 months and 8 months of age. Normal age- and sex-matched C57BL/6 mice will be used as controls.
Quality Control Description:
RNA will be analyzed by OD 260/280 and by agarose gel.
Quality Control Types:
biological_replicate
Replicate Description:
Three mouse brains will be analyzed for each data point.
Replicate Types:
biological_replicate
Experimental Factors:
Conditions that are tested in the experiment. At least one is required. Experimental factors are the independent variables in the experiment.
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Factor Name Description Factor Category
PPT1 knockout PPT1 knockout vs. wild-type disease_state
age age at time of sacrifice age
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Project Samples  This section lists the samples that are associated with this project. Individual sample details can be viewed by clicking on the View Sample icon to the right of the sample. If samples are selectable for analysis or for addition to a virtual
Samples associated with this project.
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Name Description Bio-Source Extracts  
[1] Sample #1 Knockout 3 months old, male C57BL/6 Mouse 1 1
[2] Sample #2 Knockout 3 months old, female C57BL/6 Mouse 2 1
[3] Sample #3 Knockout 3 months old, female C57BL/6 Mouse 3 1
[4] Sample #4 Knockout 5 months old, male C57BL/6 Mouse 4 1
[5] Sample #5 Knockout 5 months old, female C57BL/6 Mouse 5 1
[6] Sample #6 Knockout 5 months old, female C57BL/6 Mouse 6 1
[7] Sample #7 Knockout 8 months old, male C57BL/6 Mouse 7 1
[8] Sample #8 Knockout 8 months old, female C57BL/6 Mouse 8 1
[9] Sample #9 Knockout 8 months old, male C57BL/6 Mouse 9 1
[10] Sample #10 Wild-type 3 months old, male C57BL/6 Mouse 10 1
[11] Sample #11 Wild-type 3 months old, female C57BL/6 Mouse 11 1
[12] Sample #12 Wild-type 3 months old, female C57BL/6 Mouse 12 1
[13] Sample #13 Wild-type 5 months old, male C57BL/6 Mouse 13 1
[14] Sample #14 Wild-type 5 months old, female C57BL/6 Mouse 14 1
[15] Sample #15 Wild-type 5 months old, female C57BL/6 Mouse 15 1
[16] Sample #16 Wild-type 8 months old, male C57BL/6 Mouse 16 1
[17] Sample #17 Wild-type 8 months old, female C57BL/6 Mouse 17 1
[18] Sample #18 Wild-type 8 months old, female C57BL/6 Mouse 18 1
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Project Hybridizations 

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View Hybridization View Hybridization  
Name Array Labeled Extract Hybridization Protocol  
Mouse Genome 430 2.0 Array_1_hyb Mouse Genome 430 2.0 Array_1 [1] Sample #1_le1
Mouse Genome 430 2.0 Array_2_hyb Mouse Genome 430 2.0 Array_2 [2] Sample #2_le1
Mouse Genome 430 2.0 Array_3_hyb Mouse Genome 430 2.0 Array_3 [3] Sample #3_le1
Mouse Genome 430 2.0 Array_4_hyb Mouse Genome 430 2.0 Array_4 [4] Sample #4_le1
Mouse Genome 430 2.0 Array_5_hyb Mouse Genome 430 2.0 Array_5 [5] SAmple #5_le1
Mouse Genome 430 2.0 Array_6_hyb Mouse Genome 430 2.0 Array_6 [6] Sample #6_le1
Mouse Genome 430 2.0 Array_7_hyb Mouse Genome 430 2.0 Array_7 [7] Sample #7_le1
Mouse Genome 430 2.0 Array_8_hyb Mouse Genome 430 2.0 Array_8 [8] Sample #8_le1
Mouse Genome 430 2.0 Array_9_hyb Mouse Genome 430 2.0 Array_9 [9] Sample #9_le1
Mouse Genome 430 2.0 Array_10_hyb Mouse Genome 430 2.0 Array_10 [10] Sample #10_le1
Mouse Genome 430 2.0 Array_11_hyb Mouse Genome 430 2.0 Array_11 [11] Sample #11_le1
Mouse Genome 430 2.0 Array_12_hyb Mouse Genome 430 2.0 Array_12 [12] Sample #12_le1
Mouse Genome 430 2.0 Array_13_hyb Mouse Genome 430 2.0 Array_13 [13] Sample #13_le1
Mouse Genome 430 2.0 Array_14_hyb Mouse Genome 430 2.0 Array_14 [14] Sample #14_le1
Mouse Genome 430 2.0 Array_15_hyb Mouse Genome 430 2.0 Array_15 [15] Sample #15_le1
Mouse Genome 430 2.0 Array_16_hyb Mouse Genome 430 2.0 Array_16 [16] Sample #16_le1
Mouse Genome 430 2.0 Array_17_hyb Mouse Genome 430 2.0 Array_17 [17] Sample #17_le1
Mouse Genome 430 2.0 Array_18_hyb Mouse Genome 430 2.0 Array_18 [18] Sample #18_le1
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Project Reference Files
File Name Size
Hofmann.DTT 2.10 Gb
SignalCalls052406.TXT 6.13 Mb
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