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Genome of Mus spretus

ABSTRACT: Genome of Mus spretus

PROVIDER: PRJEB11535 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1101750.fastq.gz	Fastqsanger.gz
	ERR1101750_1.fastq.gz	Fastqsanger.gz
	ERR1101750_2.fastq.gz	Fastqsanger.gz

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Environmental pollution assessment using Mus spretus

2013-12-31 | GSE33663 | GEO

Environmental pollution assessment using Mus spretus

Project description:We evaluated the suitability of high-throughput transcriptomics approach to monitor terrestrial ecosystems. Free-living Mus spretus from several polluted sites of Huelva (Andalusia, SW Spain) were compared with mice from DoM-CM-1ana Biological Reserve (M-bM-^@M-^\Santa OlallaM-bM-^@M-^] lagoon (SOL) used as negative control). As most popular bioindicators, M. spretus is poorly represented in gene databases, therefore limiting the use of genomics in ecotoxicological studies. To solve this problem, we used microarrays produced from mRNAs of M. musculus. Specifically we used the One-Color Gene Expression Platform commercialized by Agilent. Gene expression in Mus spretus liver was assessed in mice from 5 sites of the Spanish Southwest. Five independent experiments were performed. The arrays were hybridized with labelled cRNA samples made from pooled livers of 9 mice per sampling site. We made 4 technichal repetitions per sample.

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RNA-seq data from liver tissues of Mus spretus (SPRET/EiJ) and Mus caroli (Caroli/EiJ)

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Analysis of differential gene expression in Mus spretus mice exposed to p,p’-DDE

Project description:The complexity of environmental systems requires the use of holistic methodologies to conduct studies of contamination effects over individuals who inhabit specific polluted areas. Microarrays are an appropriate tool since they allow the simultaneous expression analysis of thousand genes. As an omic and unbiased technology, it allows for the identification of novel biological responses within certain environmental conditions. A commercial microarray based on probes of the Mus musculus entire genome has been used in order to study transcriptional changes in M. spretus mice exposed to p,p’-DDE, a metabolic by-product of the organochlorine pesticide DDT, whose use is nowadays limited due to the hazardous environmental impact it causes. The success of this approach lies in the high phylogenetic closeness between M. spretus, a species of large environmental interest, whose genome is not sequenced, and the laboratory mouse M. musculus. The results obtained with these heterologous microarrays, verified by qRT-PCR, indicate that the exposed mice to this compound present alterations in their gene expression profiles relative to control animals. Based on the data obtained herein, it can be inferred that mice exposed to p,p’-DDE show alterations in lipids and carbohydrates metabolism, in the immune response, cell cycle control and signaling and molecular transport processes.

2018-06-05 | GSE103767 | GEO

Genome-wide analysis of alternative splicing evolution among Mus subspecies

Project description:We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse. We sequenced the testis transcriptomes of three Mus musculus subspecies and Mus spretus using Illumina technology. On the basis of a genome-wide analysis of read coverage differences among subspecies, we identified several hundred candidate alternatively spliced regions.

2010-02-28 | E-GEOD-18905 | biostudies-arrayexpress

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Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

Project description:We analyzed KDM1A (LSD1) occupancy in the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to distiguish genome DNA from the Xi. We found a possible physical and/or functional regulation of KDM1A during the X chromosome reactivation in the intiation site on the Xi.

2022-01-01 | GSE157479 | GEO

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