Mus musculus
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PROVIDER: PRJNA190707 | ENA |
REPOSITORIES: ENA
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Project description:We create catalogues of genes showing significant strain, parent-of-origin, dominance, sex effect in inbreds and reciprocal F1 hybrids of three wild-derived strains (CAST, PWK, WSB) across 4 different tissues (brain, kidney, liver, and lung) We used microarrays to validate the Brain results of RNAseq from inbred and F1 of 3 by 3 diallel.
2013-05-01 | GSE44555 | GEO
Project description:We create catalogues of genes showing significant strain, parent-of-origin, dominance, sex effect in inbreds and reciprocal F1 hybrids of three wild-derived strains (CAST, PWK, WSB) across 4 different tissues (brain, kidney, liver, and lung) We used microarrays to validate the Brain results of RNAseq from inbred and F1 of 3 by 3 diallel. Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix.
2013-05-01 | E-GEOD-44555 | biostudies-arrayexpress
Project description:Collaborative Cross (CC) mouse embryonic fiborolasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with type I, II and III recombinant mouse interferon.
2014-05-27 | GSE53057 | GEO
Project description:To characterize the genetic basis of hybrid male sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven M-bM-^@M-^Xhotspots,M-bM-^@M-^Y seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL - but not cis eQTL - were substantially lower when mapping was restricted to a M-bM-^@M-^XfertileM-bM-^@M-^Y subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. Gene expression was measured in whole testis in males aged 70(M-BM-15) days. Samples include 294 WSB/EiJ x PWD/PhJ F2s, 11 PWD/PhJ x WSB/EiJ F2s, 8 WSB/EiJ, 8 PWD/PhJ, 6 PWD/PhJ x WSB/EiJ F1s and 4 WSB/EiJ x PWD/PhJ F1s.
2014-05-01 | E-GEOD-54089 | biostudies-arrayexpress
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. The genetic profile of these emerging lines reveals high diversity, balanced allele frequencies, and well-distributed recombination – all ideal qualities for a mapping panel. We have mapped white spot, a discrete trait; body weight, a highly polygenic complex trait; and more than 11,000 liver gene expression traits. These analyses provide a glimpse of the potential mapping power and resolution of the CC. The goal of this project was to identify eQTLs for genome-wide gene expression from liver tissue in pre-CC mice. Gene expression profiling from liver tissue from pre-CC males. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 4-11 generations. One animal was sampled from 157 pre-CC strain. Hybridizations were performed at the Gene Expression Core Facility at The Jackson Laboratory. Samples were divided in six batches of about 11 to 24 samples. Two batches were performed per day. Probe-level data was summarized by a custom CDF file based on Ensembl genes (NCBI 37, Ensembl 49; htttp://brainarray.mbni.med.umich.edu). The parental strains are not part of this submission.
2010-12-01 | E-GEOD-22297 | biostudies-arrayexpress
Project description:We used a reciprocal cross of Mus musculus and M. domesticus in which F1 males are sterile in one direction and fertile in the other direction, in order to associate expression differences with sterility. Four different crosses were performed. A cross between two strains within each mouse species (M. musculus, PWK/PhJ and CZECHII/EiJ; M. domesticus, LEWES/EiJ and WSB/EiJ). And two reciprocal crosses between a domesticus (LEWES/EiJ) and a musculus (PWK/PhJ) strain. The cross between a musculus female and a domesticus male produces sterile male offspring - whereas all other crosses produced fertile male offspring. Testis tissue from three male mice (60 days old) from all four crosses were analysed on the Affymetrix MG 430.2. Array.
2010-10-05 | E-GEOD-17684 | biostudies-arrayexpress
Project description:The Collaborative Cross (CC) recombinant inbred panel was conceived as an ideal resource for mammalian system genetics. The pre-CC is a proof-of-concept experiment involving CC lines that have undergone at least five generations of inbreeding. Siblings from these lines were each involved in one of four distinct phenotyping arms, then genotyped on a high-density Affymetrix platform. These mice were initially described in the following reference. Genome Research 2011 Aug;21(8):1213-22 (PMID: 21406540). The goal of this specific project was to identify gene expression QTL using lung tissue from pre-CC mice that were sensitized and challenged with house dust mite allergen (namely, Der p 1). We analyzed whole lung RNAs from 138 pre-Collaborative Cross mice using Illumina WG6v2 arrays. Pre-Collaborative Cross (CC) mice are partially inbred strains created by intercrossing eight founder (parental) strains: 129S1/SvImJ, (129S1), A/J (AJ), C57BL/6J (B6), CAST/Ei (CAST), NOD/LtJ (NOD), NZO/H1LtJ (NZO), PWK/Ph (PWK), and WSB/Ei (WSB). Sister-brother mating in 220 families was done for 5-12 generations. One animal was sampled from 138 unique pre-CC strains, each designated by the prefix OR which denotes Oak Ridge National Laboratory as the original source of these mice. The parental strains are not part of this submission. Hybridizations were performed at the National Human Genome Research InstituteM-bM-^@M-^Ys Gene Expression Core Facility.The resulting data were initially processed using Illumina Genome Studio software and then imported into R (v2.9.2) for post-processing. Normalization was conducted using RMA with quantile normalization and log2 transformation.
2013-11-15 | E-GEOD-51768 | biostudies-arrayexpress
Project description:Mus musculus breed:CAST/WSB Raw sequence reads
| PRJNA280976 | ENA
Project description:Collaborative Cross (CC) mouse embryonic fibroblasts (MEF) cells obtained from the eight Founder animals [PWK/PhJ, NZO/HILtJ, NOD/ShiLtJ, WSB/EiJ, A/J, CAST, C57BL/6J, and 129/SvlmJ] were immortalized and the cell lines used to assess differences in transcriptional responses following treatment with mouse recombinant IFNg and IL28. We collected transcriptome profiles for 8 CC MEF cell lines stimulated with either IFNg or IL28 for a total of 16 different biological conditions. Treated and mock samples were collected at 18 hr post-treatment and RNAs extracted and subjected to microarray.
2016-05-26 | E-MTAB-4690 | biostudies-arrayexpress
Project description:Purpose: To investigate the diet- or strain-dependence of liver transcriptome in eight Diversity Outbred (DO) founder strains [A/J, C57BL/6J (B6), 129S1/SvImJ (129), NOD/ShiLtJ (NOD), NZO/HILtJ (NZO), and three wild-derived strains CAST/EiJ (CAST), PWK/PhJ (PWK), and WSB/EiJ (WSB)] Methods: Total RNA from eight DO founder strains was extracted from snap frozen liver using Maxwell® 16 LEV simplyRNA Tissue Kit (Promega) according to the manufacturer’s protocol. The quality and amount of liver RNA was evaluated using a qubit RNA assay (Invitrogen R11490) and run on an Biorad Bioanalyzer Chip to verify RNA integrity. RNASeq library was prepared by using Illumina TruSeq RNA library construction protocol. RNA samples from 24 mice-fed AIN-93 M diet and 24 mice-fed HFCA diet were submitted to the David H. Murdock Research Institute (DHMRI) for sequencing. The RNA-seq libraries were constructed from 1 µg total RNA after poly-A library preparation. The pooled libraries were sequenced on two lanes of the Illumina HiSeq2500 Instrument. Results: Our liver transcriptomic analysis of eight mouse strains shows that diet and genetic background have a strong effect on the liver transcriptome, which may be related to differences in cardo-metabolic traits. We calculated a gene module consisting of highly correlated transcripts that enriched the biological pathway and provided a searchable database of liver transcript profiles. To further investigate the association of hepatic gene modules with cardio-metabolic traits, Fmo3, a key enzyme in the production of trimethylamine N-oxide (TMAO), and Nox4, which showed strong association with plasma TMAO and liver triglyceride, were identified as the highest expressed in the laboratory-like inbred strains (B6, 129 and NZO) and the lowest expressed transcripts in the CAST strain. We found differences in the production of TMAO and liver triglyceride, which contributes to metabolic syndrome, depending on genetic backgrounds. Conclusions: Our study provide a valuable data resource to the research community and show that liver transcriptomic analysis identified diet- or strain-specific pathways to pathogenesis of metabolic syndrome.
2021-09-15 | GSE159992 | GEO