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Title: Transcription profiling of two mouse lines displaying different phenotypes on fear conditioning to identify identify differences in gene expression in two key brain regions: amygdala and hippocampus      
availability:
available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
06-10-2011
ID:
E-GEOD-4035
description:
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 received. Upon being placed back in the context, mice exhibit freezing behavior, which is a species-specific response to fear. We have used selective breeding to produce lines of mice with high or low levels of freezing behavior. We are able to identify alleles that govern the genetic variability for FC by using chromosomal markers in these 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.,We will compare gene expression in the amygdala and hippocampus (brain regions known to be relevant to fear behavior) from the two lines of mice and use Bayesian statistics in an effort to identify gene expression that affects fear behavior.,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. Selective breeding changes the frequency of trait relevant (FC) alleles. A relevant allele is expected to increase in one selected line and decrease in the oppositely selected line. Some trait relevant alleles are expected cause changes in the level of expression at particular genes.,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.
keywords:
transcription profiling by array
format:
HTML
storedIn:
Array Express
qualifier:
not compressed
accessType:
landing page
authorization:
none
authentication:
none
primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4035
format:
JSON
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-4035.json
format:
XML
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-4035.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/