Hippocampal gene expression analysis highlights Ly6a/Sca-1 as candidate gene for previously mapped novelty induced behaviors in mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE29289 | GEO | 2011/07/01
SECONDARY ACCESSION(S): PRJNA138613
REPOSITORIES: GEO
Similar Datasets
Project description:Using gene expression analysis to narrow down a behavioral QTL Hippocampus (left) dissected from frozen tissue of female CSS15F2 population using a punching procedure. N=37
2011-07-01 | E-GEOD-29289 | biostudies-arrayexpress
Project description:In this study, we show that the covariance between behavior and gene expression in the brain can help further unravel the determinants of neurobehavioral traits. Previously, a QTL for novelty induced motor activity levels was identified on murine chromosome 15 using consomic strains. With the goal of narrowing down the linked region and possibly identifying the gene underlying the quantitative trait, gene expression data from this F(2)-population was collected and used for expression QTL analysis. While genetic variation in these mice was limited to chromosome 15, eQTL analysis of gene expression showed strong cis-effects as well as trans-effects elsewhere in the genome. Using weighted gene co-expression network analysis, we were able to identify modules of co-expressed genes related to novelty induced motor activity levels. In eQTL analyses, the expression of Ly6a (a.k.a. Sca-1) was found to be cis-regulated by chromosome 15. Ly6a also surfaced in a group of genes resulting from the network analysis that was correlated with behavior. Behavioral analysis of Ly6a knock-out mice revealed reduced novelty induced motor activity levels when compared to wild type controls, confirming functional importance of Ly6a in this behavior, possibly through regulating other genes in a pathway. This study shows that gene expression profiling can be used to narrow down a previously identified behavioral QTL in mice, providing support for Ly6a as a candidate gene for functional involvement in novelty responsiveness.
| S-EPMC3108967 | biostudies-literature
Project description:At early developmental stages, limb bud mesodermal undifferentiated cells are morphologically indistinguishable. Although the identification of several mesodermal skeletal progenitor cell populations has been recognized, in advanced stages of limb development here we identified and characterized the differentiation hierarchy of two new early limb bud subpopulations of skeletal progenitors defined by the differential expression of the SCA-1 marker. Based on tissue localization of the mesenchymal stromal cell-associated markers (MSC-am) CD29, Sca-1, CD44, CD105, CD90, and CD73, we identified, by multiparametric analysis, the presence of cell subpopulations in the limb bud capable of responding to inductive signals differentially, namely, sSca+ and sSca- cells. In concordance with its gene expression profile, cell cultures of the sSca+ subpopulation showed higher osteogenic but lower chondrogenic capacity than those of sSca-. Interestingly, under high-density conditions, fibroblast-like cells in the sSca+ subpopulation were abundant. Gain-of-function employing micromass cultures and the recombinant limb assay showed that SCA-1 expression promoted tenogenic differentiation, whereas chondrogenesis is delayed. This model represents a system to determine cell differentiation and morphogenesis of different cell subpopulations in similar conditions like in vivo. Our results suggest that the limb bud is composed of a heterogeneous population of progenitors that respond differently to local differentiation inductive signals in the early stages of development, where SCA-1 expression may play a permissive role during cell fate.
| S-EPMC8322737 | biostudies-literature
Project description:A QTL intercross was performed bewteen C57BL/6J and KK/HIL for albuminurea, asthma and cardiovascular related phenotypes. Several QTL were identified for most phenotypes. We performed microarray analysis from liver samples to identify genes differentially expressed between the parental strains. The results helped us narrow down the QTL and identify the candidate genes based on differential expression between the parental strains.
2012-10-18 | GSE37429 | GEO
Project description:In order to narrow candidate QTL loci into relevant genes driving disease differences, we assessed transcriptional differences across the pre-CC population used to map phenotypic QTL. We integrate this normalized expression data with polymorphisms underneath a candidate locus to arrive at a high priority candidate gene which had genetic variants private to the causal haplotype and also had expression strongly correlated with the appropriate trait (SARS-CoV viral lung load at 4 DPI).
2017-03-31 | GSE93283 | GEO
Project description:A QTL analysis between inbred mouse strains MRL/MpJ and SM/J was performed to identify genetic loci influencing high-density lipoprotein (HDL) cholesterol and triglycerides (TG) at eight weeks of age in F2 mice fed a chow diet. In order to narrow down lists of candidate genes, expression levels from liver tissue were used to test for differential expression among parental and F1 strains and to scan for eQTL in F2 animals. We provide evidence for Mppe1 (Chr 18) as an HDL QTL candidate gene and Cyp2d26 (Chr 15) as a TG QTL candidate gene.
2011-11-28 | GSE25322 | GEO
Project description:By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele.
2012-04-01 | GSE35762 | GEO
Project description:ObjectiveThis study included 54-month-old children with a history of institutional care. Our goal was to: (1) examine differences in indiscriminate social behaviors in children with a history of institutional care compared with home-reared children; (2) test whether foster care reduces indiscriminate social behaviors in a randomized controlled trial; and (3) examine early predictors of indiscriminate behaviors.MethodsParticipants were 58 children with a history of institutional care and 31 never-institutionalized control (NIG) subjects enrolled in a randomized controlled trial of foster care for institutional care, assessed from toddlerhood to 54 months. Indiscriminate social behaviors were measured naturalistically by using the Stranger at the Door procedure.ResultsIn the Stranger at the Door procedure, children with a history of institutional care left with a stranger at higher rates than NIG subjects (33% vs. 3.5%; P < .001). Children in the care as usual group left more than NIG subjects (41.9% vs. 3.6%; P ≤ .001). The differences between the foster care group (24.1%) and the care as usual group and between foster care group and NIG were not significant. In a logistic regression, early disorganized attachment behaviors, baseline developmental quotient, and caregiving quality after randomization contributed to variance at 54 months. In the same analysis using only children with a history of institutional care, only disorganized attachment contributed significantly to 54-month indiscriminate social behaviors (Exp[B] = 1.6 [95% confidence interval: 1.1-2.5]).ConclusionsObserved socially indiscriminate behaviors at 54 months were associated with prolonged exposure to institutional care. Young children raised in conditions of deprivation who fail to develop organized attachments as toddlers are at increased risk for subsequent indiscriminate behaviors.
| S-EPMC3934326 | biostudies-literature
Project description:A QTL intercross was performed bewteen C57BL/6J and KK/HIL for albuminurea, asthma and cardiovascular related phenotypes. Several QTL were identified for most phenotypes. We performed microarray analysis from liver samples to identify genes differentially expressed between the parental strains. The results helped us narrow down the QTL and identify the candidate genes based on differential expression between the parental strains. At 8 weeks of age, the large lobe of the liver from 3 male and 3 females C57BL/6J and KK/HIJ (12 mice total) was collected. The mice were separated individuallly for 3 days and fasted for 4 hours prior to the tissue collection. The mice were sacrificed by cervically dislocation and perfused with PBS prior to the liver collection.
2012-10-18 | E-GEOD-37429 | biostudies-arrayexpress
Project description:By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele. Expression profiling with the rice 44K-Agilent microarray (Agilent-028517) was conducted using RNAs extracted from the 30-day-old vegetative stem of the corresponding lines. Each dataset was obtained from three biological replicates.
2012-03-31 | E-GEOD-35762 | biostudies-arrayexpress