View Project palme-affy-mouse-198967

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:	hippocampus	Sample Detail	false
Cell Type:	mixed neural cells	Hybridization Detail	false
Study Type:	pharmacogenomic	Measurement Detail	false
Disease/Condition:	normal
Replicates:	24
Expected Samples:

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Investigator Contact Detail
Name	Dr. Abraham A Palmer
Institution:	University of Chicago
Street Address:	920 E 58th St
	CLSC Room 507D
City, State/Province:	Chicago , IL
Zip/Postal Code:	60637
Country:	United States
Work Phone:	773-834-2897
Fax:	773-834-0505
E-mail:	aap@uchicago.edu

Proposal Detail

Grant:

1K01MH070933-01

Status:

Public

Service Type:

Start to Finish Profiling

IACUC:

AAAA3522

IACUC date:

2005-08-17

Study Relevance:

Fear conditioning (FC) is a behavioral paradigm that measures an animal's ability to learn fear related information. FC is measured by pairing a mild foot-shock with the surroundings in which the shock was recieved. Upon being placed back in the context, mice exhibit freezing behavior, which is a species-specific response to fear. We have previously used selective breeding to produce lines of mice with high or low levels of freezing behavior. This experiment is a replication of a previous experiment that produced lines of mice with high or low levels of freezing behavior. These lines derive from different progenitor mouse strains. We are able to identify alleles that govern the genetic variability for FC by using chromosomal markers in these selected lines. Using microarrays, we will identify differences in gene expression in two key brain regions: amygdala and hippocampus. Gene expression differences and data regarding chromosomal regions involved in the behavior will be compared to identify particular genes that are both differentially expressed and whose expression is governed by alleles that fall into critical chromosomal regions.

Hypothesis:

We hypothesize that selection has acted in part by changing the frequency of alleles that cause differential expression of key genes in the amygdala and hippocampus of our selected lines. Slective breeding changes the frequency of trait relevand (FC) alleles. A relevant allele is expected to increas in one selected line and decrease in the oppositely selected line. Some trait relevant alleles are expected to cause changes in the level of expression at particular genes.

Specific Aim:

We will compare gene expresion in the amygdala and hippocampus (brain regions known to be relevant to fear behavior) from the these two lines of mice and to the those in the previous experiment. Bayesian statistics will be used in an effort to identify gene expression that affects fear behavior.

Experimental Procedure and Design:

Amygdala and hippocampus will be rapidly dissected out of experimentally naïve mice from each line. Naïve mice will be used for expression studies since the behavior of the mice in the FC test can be reliably anticipated due to their lineage. We have practiced these procedures, and can accurately and reproducibly remove these regions in less than 5 minutes. Different mice will be used to collect each brain region, since the dissection of hippocampus disrupts the removal of amygdala. We will collect enough samples from each region to accommodate a total of 6 microarrays per brain region, per line, thus we will use a total of 24 microarrays. We anticipate that a single brain region will be sufficient to for a microarray. However, we propose to utilize three samples per microarray, because this will reduce variability due to environmental factors and due to slight variability in our dissection procedures. Once this tissue is removed, we will isolate RNA for shipment to the Microarray consortium. We will also collect spleens from each subject as a source of genomic DNA, in order to permit direct comparison of genotype and expression phenotypes. Once we have the results of the microarray analysis, we use WebQTL.org to identify the chromosomal locations of alleles that are know to influence the expression of genes for which we have found differential expression. We will then superimpose this information on trait relevant chromosomal regions identified from our selected lines. This will allow us to rapidly identify genes which may account for genetic variability in FC due to differential expression. Such genes will then be subjected to further study.

Experimental Factors:

Conditions that are tested in the experiment. At least one is required. Experimental factors are the independent variables in the experiment.

Factor Name	Description	Factor Category
Fear Behavior	High freezing mice are compared to lo...	individual_genetic_characteristic

Project Samples

Samples associated with this project.

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Name	Description	Extracts
Hippocampus 1	Low Freezing	1
Hippocampus 2	Low Freezing	1
Hippocampus 3	Low Freezing	1
Hippocampus 4	Low Freezing	1
Hippocampus 5	Low Freezing	1
Hippocampus 6	Low Freezing	1
Hippocampus 7	High Freezing	1
Hippocampus 8	High Freezing	1
Hippocampus 9	High Freezing	1
Hippocampus 10	High Freezing	1
Hippocampus 11	High Freezing	1
Hippocampus 12	High Freezing	1
Amygdala 1	Low Freezing	1
Amygdala 2	Low Freezing	1
Amygdala 3	Low Freezing	1
Amygdala 4	Low Freezing	1
Amygdala 5	Low Freezing	1
Amygdala 6	Low Freezing	1
Amygdala 7	High Freezing	1
Amygdala 8	High Freezing	1
Amygdala 9	High Freezing	1
Amygdala 10	High Freezing	1
Amygdala 11	High Freezing	1
Amygdala 12	High Freezing	1

Project Hybridizations

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Name	Array	Labeled Extract
Mouse Genome 430 2.0 Array_1_hyb	Mouse Genome 430 2.0 Array_1	Hippocampus 1_le1
Mouse Genome 430 2.0 Array_2_hyb	Mouse Genome 430 2.0 Array_2	Hippocampus 2_le1
Mouse Genome 430 2.0 Array_3_hyb	Mouse Genome 430 2.0 Array_3	Hippocampus 3_le1
Mouse Genome 430 2.0 Array_4_hyb	Mouse Genome 430 2.0 Array_4	Hippocampus 4_le1
Mouse Genome 430 2.0 Array_5_hyb	Mouse Genome 430 2.0 Array_5	Hippocampus 5_le1
Mouse Genome 430 2.0 Array_6_hyb	Mouse Genome 430 2.0 Array_6	Hippocampus 6_le1
Mouse Genome 430 2.0 Array_7_hyb	Mouse Genome 430 2.0 Array_7	Hippocampus 7_le1
Mouse Genome 430 2.0 Array_8_hyb	Mouse Genome 430 2.0 Array_8	Hippocampus 8_le1
Mouse Genome 430 2.0 Array_9_hyb	Mouse Genome 430 2.0 Array_9	Hippocampus 9_le1
Mouse Genome 430 2.0 Array_10_hyb	Mouse Genome 430 2.0 Array_10	Hippocampus 10_le1
Mouse Genome 430 2.0 Array_11_hyb	Mouse Genome 430 2.0 Array_11	Hippocampus 11_le1
Mouse Genome 430 2.0 Array_12_hyb	Mouse Genome 430 2.0 Array_12	Hippocampus 12_le1
Mouse Genome 430 2.0 Array_13_hyb	Mouse Genome 430 2.0 Array_13	Amygdala 1_le1
Mouse Genome 430 2.0 Array_14_hyb	Mouse Genome 430 2.0 Array_14	Amygdala 2_le1
Mouse Genome 430 2.0 Array_15_hyb	Mouse Genome 430 2.0 Array_15	Amygdala 3_le1
Mouse Genome 430 2.0 Array_16_hyb	Mouse Genome 430 2.0 Array_16	Amygdala 4_le1
Mouse Genome 430 2.0 Array_17_hyb	Mouse Genome 430 2.0 Array_17	Amygdala 5_le1
Mouse Genome 430 2.0 Array_18_hyb	Mouse Genome 430 2.0 Array_18	Amygdala 6_le1
Mouse Genome 430 2.0 Array_19_hyb	Mouse Genome 430 2.0 Array_19	Amygdala 7_le1
Mouse Genome 430 2.0 Array_20_hyb	Mouse Genome 430 2.0 Array_20	Amygdala 8_le1
Mouse Genome 430 2.0 Array_21_hyb	Mouse Genome 430 2.0 Array_21	Amygdala 9_le1
Mouse Genome 430 2.0 Array_22_hyb	Mouse Genome 430 2.0 Array_22	Amygdala 10_le1
Mouse Genome 430 2.0 Array_23_hyb	Mouse Genome 430 2.0 Array_23	Amygdala 11_le1
Mouse Genome 430 2.0 Array_24_hyb	Mouse Genome 430 2.0 Array_24	Amygdala 12_le1

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