Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of the testicular transcriptome of chromosomes 2, X, Y and the mitochondrial genome between two mouse species

ABSTRACT: We used tiling arrays to compare the testicular expression of chromosomes 2, X, Y and the mitochondrial genome between Mus m. domesticus and Mus spretus. We found an excess of dysregulated non-coding RNAs on chromosome 2. This group consists of intronic antisense RNAs, intergenic RNAs and also premature forms of PIWI-interacting RNAs (piRNAs). The unique transcriptional regulation in spermatogenesis is a characteristic of chromosome X. It is subject to meiotic transcriptional silencing, which is accompanied by generating X-chromosomal retrogenes on autosomes. We found striking dysregulation of the G6pdx - G6pd2 parental-retrogene pair between the mouse species. The postmeiotic expression of G6pdx in Mus spretus points out the continuous evolution of X chromosome silencing and provides clue for regulatory changes, which accompanies the out-of-X gene flow. Comparison between 3 samples of Mus spretus and 3 samples of Mus m. domesticus (C57BL/6J, B6). The supplementary file 'GSE19633_Spr_v_B6.bed' contains the chromosomal localizations of the probes together with logFC and adjusted P values.

ORGANISM(S): Mus spretus

SUBMITTER: Robert Ivanek

PROVIDER: E-GEOD-19633 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of the testicular transcriptome of chromosomes 2, X, Y and the mitochondrial genome between two mouse species

Project description:We used tiling arrays to compare the testicular expression of chromosomes 2, X, Y and the mitochondrial genome between Mus m. domesticus and Mus spretus. We found an excess of dysregulated non-coding RNAs on chromosome 2. This group consists of intronic antisense RNAs, intergenic RNAs and also premature forms of PIWI-interacting RNAs (piRNAs). The unique transcriptional regulation in spermatogenesis is a characteristic of chromosome X. It is subject to meiotic transcriptional silencing, which is accompanied by generating X-chromosomal retrogenes on autosomes. We found striking dysregulation of the G6pdx - G6pd2 parental-retrogene pair between the mouse species. The postmeiotic expression of G6pdx in Mus spretus points out the continuous evolution of X chromosome silencing and provides clue for regulatory changes, which accompanies the out-of-X gene flow.

2011-02-16 | GSE19633 | GEO

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

Genome-wide transcripts from X chromosome by high throughput sequencing [RNA-Seq]

Project description:We analyzed a transcriptional landscape of 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 monitor allele-specific transcripts from the Xi. We could capture the earliest phase of X chromosome reactivation and found that a subset of genes clustered near the centromere display an early reactivation on the Xi.

2022-01-01 | GSE157481 | GEO

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

2006-12-13 | GSE2597 | GEO

ChIP-Seq analysis of CCCTC-binding factor (CTCF) binding in rodents

Project description:We explored the microevolutionary trends of CTCF binding evolution by preforming ChIP-seq experiments in five closely related Mus strains, subspecies and species: Mus musculus domesticus, Mus musculus castaneus, Mus spretus, Mus caroli and Mus pahari. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. Complementary RNA-seq data from this same study have been deposited in ArrayExpress under accession numebr E-MTAB-5768 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5768 ).

2018-03-06 | E-MTAB-5769 | biostudies-arrayexpress

Contrasting patterns of expression divergence in early and late stages of population divergence in mice

Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. The design we employed is a reference design. All tissues were hybridized against a pool of that same tissue from 9 C57BL6 mice. All mice were roughly 12 weeks of age. To control for biological variation, we have used several individual males from each sub-species. RNA was isolated from three different organs, namely brain, liver/kidney and testis.

2010-06-30 | E-GEOD-2597 | biostudies-arrayexpress

Uterus and placenta gene expression at 10.5 days of pregnancies in control (B6 mice) and R3 IRCS mice

Project description:R3 IRCS have a 6 Mb fragment of mouse chromosome 1 originating from Mus spretus; they display a increase rate of embryonic mortality

2012-02-01 | GSE32640 | GEO

Interspecific Introgressive Origin of Genomic Diversity in the House Mouse

Project description:We report on a genome-wide scan for introgression in the house mouse (Mus musculus domesticus) involving the Algerian mouse (Mus spretus), using 20 samples from the ranges of sympatry and allopatry. Our analysis reveals significant variability in introgression signatures along the genomes, as well as across the samples. We find that fewer than half of the chromosomes in each genome harbor all detectable introgression. Further, a surprising result is that European mice carry more M. spretus alleles than the sympatric African ones. Using the length distribution and sharing patterns of introgressed genomic tracts across the samples, we propose three hypotheses. First, at least three distinct hybridization events involving M. spretus have occurred, one of which is ancient, and the other two are recent. Second, several of the inferred introgressed tracts contain genes that are likely to confer adaptive advantage. Third, introgressed tracts might contain driver genes that determine the evolutionary fate of those tracts. Further, our analysis revealed introgressed genes of functional importance, including the Vkorc1 gene, which is implicated in rodenticide resistance, and olfactory receptor genes. Our findings highlight the extent and role of introgression in nature, and call for careful analysis and interpretation of house mouse data in evolutionary and genetic studies. Six wild M. m. domesticus samples were genotyped using the Affymetrix Mouse Diversity Genotyping Array.

2014-11-01 | E-GEOD-62906 | biostudies-arrayexpress

Interspecific Introgressive Origin of Genomic Diversity in the House Mouse

2014-11-01 | GSE62906 | GEO

Variation in mouse chemical signals is genetically controlled and environmentally modulated

Project description:Urine proteomes of the house mouse (Mus musculus musculus, M. m. domesticus, M. m. castaneus).

2023-07-20 | PXD037086 | Pride