Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq from amygdala tissue of 205 heterogeneous stock rats

ABSTRACT: We measured amygdala gene expression in 205 Heterogeneous Stock (N:HS) rats. These animals were part of a larger cohort that were extensively phenotyped and genotyped and originally published in PMID: 23708188, although the gene expression data here were not included in that study.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Rattus norvegicus

SUBMITTER: Richard Mott

PROVIDER: E-MTAB-12693 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

Baud Amelie A Hermsen Roel R Guryev Victor V Stridh Pernilla P Graham Delyth D McBride Martin W MW Foroud Tatiana T Calderari Sophie S Diez Margarita M Ockinger Johan J Beyeen Amennai D AD Gillett Alan A Abdelmagid Nada N Guerreiro-Cacais Andre Ortlieb AO Jagodic Maja M Tuncel Jonatan J Norin Ulrika U Beattie Elisabeth E Huynh Ngan N Miller William H WH Koller Daniel L DL Alam Imranul I Falak Samreen S Osborne-Pellegrin Mary M Martinez-Membrives Esther E Canete Toni T Blazquez Gloria G Vicens-Costa Elia E Mont-Cardona Carme C Diaz-Moran Sira S Tobena Adolf A Hummel Oliver O Zelenika Diana D Saar Kathrin K Patone Giannino G Bauerfeind Anja A Bihoreau Marie-Therese MT Heinig Matthias M Lee Young-Ae YA Rintisch Carola C Schulz Herbert H Wheeler David A DA Worley Kim C KC Muzny Donna M DM Gibbs Richard A RA Lathrop Mark M Lansu Nico N Toonen Pim P Ruzius Frans Paul FP de Bruijn Ewart E Hauser Heidi H Adams David J DJ Keane Thomas T Atanur Santosh S SS Aitman Tim J TJ Flicek Paul P Malinauskas Tomas T Jones E Yvonne EY Ekman Diana D Lopez-Aumatell Regina R Dominiczak Anna F AF Johannesson Martina M Holmdahl Rikard R Olsson Tomas T Gauguier Dominique D Hubner Norbert N Fernandez-Teruel Alberto A Cuppen Edwin E Mott Richard R Flint Jonathan J

Nature genetics 20130526 7

Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpect ...[more]

PMID: 23708188

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Project description:Fly strains were obtained from the Bloomington Stock Center. The chromosomes containing the gene deletion mod(mdg4)L3101 {y[1] w[1118]; P{w[+mC]=lacW}mod(mdg4)[L3101]/TM3, Ser[1]}, HP1 {In(1)w[m4h]; Su(var)205[5]/In(2L)Cy,In(2R)Cy, Cy[1]}, mod(mdg4)G16853 {w[1118]; P{w[+mC]=EP}mod(mdg4)[G16853]/TM6C, Sb[1]}, and Jil-1Scim {y[1]; P{y[+mDint2] w[BR.E.BR]=SUPor-P}JIL-1[Scim] ry[506]} were introgressed into the genetic background y[1]; bw[1]; e[4]; ci[1] ey[R] to generate the strains Mod(mdg4)/+, Su(var)205/+ and JIL-1/+. All females used in the introgression were collected within 7 hours after eclosion. For gene expression analyses, flies were grown in incubators at 25°C, 65% of relative humidity, and constant light. Newly emerged male adults flies harboring the mutations and the Y chromosomes Yohio and Ycongo(Mod(mdg4)/+;Yohio and Mod(mdg4)/+;Ycongo, Su(var)205/+;Yohio and Su(var)205/+;Ycongo, and JIL-1/+;Yohio and JIL-1/+;Ycongo) were collected and aged for 2 days at the same rearing condition before they were flash-frozen in liquid nitrogen. Four replicas of each sample were collected and stored at -80°C. Total RNA was extracted from whole flies using TRIzol (Life Technologies). The synthesis of cDNA and its labeling with fluorescent dyes (Cy3 and Cy5) as well as hybridization reactions were carried out using 3DNA protocols and reagents (Genisphere). The genetic interaction of the Y chromosome and the mutation was studied by the following contrasts: 1) male flies Mod(mdg4)/+;Yohio versus male flies Mod(mdg4)/+;Ycongo; 2) male flies Su(var)205/+;Yohio versus male flies Su(var)205/+;Ycongo; 3) male flies JIL-1/+;Yohio versus male flies JIL-1/+;Ycongo). As reference we used the same genetic background without the mutations [+/+;Ycongo (background 2) and +/+;Yohio (background 2)]. Slides were scanned using Axon 400B scanner (Axon Instruments) and GenePix Pro 6.0 software. Foreground fluorescence of dye intensities was normalized by the Loess method in Bioconductor / Limma.

Dataset Information

RNA-seq from amygdala tissue of 205 heterogeneous stock rats

Publications

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

Similar Datasets

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