Mus musculus
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ABSTRACT:
PROVIDER: PRJNA150335 | ENA |
REPOSITORIES: ENA
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Project description:Microarray analysis of male and female CD-1 mouse liver was carried out at 3, 4, and 8 wk of age to elucidate developmental changes in gene expression from the pre-pubertal period to young adulthood. A large number of sex-biased and sex-independent genes showed significant changes during this developmental period. Notably, sex-independent genes involved in cell cycle, chromosome condensation, and DNA replication were down regulated from 3 wk to 8 wk, while genes associated with metal ion binding, ion transport and kinase activity were up regulated. A majority of genes showing sex differential expression in adult liver did not display sex differences prior to puberty, at which time extensive changes in sex-specific gene expression were seen, primarily in males. Thus, in male liver, 76% of male-specific genes were up regulated and 47% of female-specific genes were down regulated from 3 to 8 wk of age, whereas in female liver 67% of sex-specific genes showed no significant change in expression. In both sexes, genes up regulated from 3 to 8 wk were significantly enriched (p < E-76) in the set of genes positively regulated by the liver transcription factor HNF4α, as determined in a liver-specific HNF4α knockout mouse model, while genes down regulated during this developmental period showed significant enrichment (p < E-65) for negative regulation by HNF4α. Significant enrichment of the developmentally regulated genes in genes subject to positive and negative regulation by pituitary hormone was also observed. Nine sex-specific transcription factors showed pubertal changes in expression and may contribute to the developmental changes that onset after 3-4 wk. Overall, the observed changes in gene expression during postnatal liver development reflect the deceleration of liver growth and the induction of specialized liver functions, with widespread changes in sex-specific gene expression primarily occurring in male liver.
2012-04-04 | GSE34782 | GEO
Project description:Microarray analysis of male and female CD-1 mouse liver was carried out at 3, 4, and 8 wk of age to elucidate developmental changes in gene expression from the pre-pubertal period to young adulthood. A large number of sex-biased and sex-independent genes showed significant changes during this developmental period. Notably, sex-independent genes involved in cell cycle, chromosome condensation, and DNA replication were down regulated from 3 wk to 8 wk, while genes associated with metal ion binding, ion transport and kinase activity were up regulated. A majority of genes showing sex differential expression in adult liver did not display sex differences prior to puberty, at which time extensive changes in sex-specific gene expression were seen, primarily in males. Thus, in male liver, 76% of male-specific genes were up regulated and 47% of female-specific genes were down regulated from 3 to 8 wk of age, whereas in female liver 67% of sex-specific genes showed no significant change in expression. In both sexes, genes up regulated from 3 to 8 wk were significantly enriched (p < E-76) in the set of genes positively regulated by the liver transcription factor HNF4M-NM-1, as determined in a liver-specific HNF4M-NM-1 knockout mouse model, while genes down regulated during this developmental period showed significant enrichment (p < E-65) for negative regulation by HNF4M-NM-1. Significant enrichment of the developmentally regulated genes in genes subject to positive and negative regulation by pituitary hormone was also observed. Nine sex-specific transcription factors showed pubertal changes in expression and may contribute to the developmental changes that onset after 3-4 wk. Overall, the observed changes in gene expression during postnatal liver development reflect the deceleration of liver growth and the induction of specialized liver functions, with widespread changes in sex-specific gene expression primarily occurring in male liver. Liver RNA isolated from the following six groups of CD-1 mice was used in the present study: 3 wk old male (M) mice (n = 10; 5 per each pool) and female (F) mice (n = 10; 5 per each pool); 4 wk old male mice (n = 12; 6 per each pool) and female mice (n = 12; 6 per each pool); 8 wk old male mice (n = 12; 6 per each pool) and female mice (n = 12; 6 per each pool). These RNA pools were used in seven separate sets of competitive hybridization experiments: 1) 3 wk M vs. 3 wk F; 2) 4 wk M vs. 4 wk F; 3) 8 wk M vs. 8 wk F; 4) 3 wk M vs. 8 wk M; 5) 4 wk M vs. 8 wk M; 6) 3 wk F vs. 8 wk F; 7) 4 wk F vs. 8 wk F. Fluorescent labeling of RNA and hybridization of the Alexa 555-labeled (green) and Alexa 647-labeled (red) aRNA samples to Agilent Mouse Gene Expression 4x44k v2 microarrays (Agilent Technology, Palo Alto, CA; catalog # G4846A-026655) were carried out, with dye swapping for each of the seven hybridization experiments to eliminate dye bias. Two microarrays, one for each mixed cDNA sample, were hybridized for each of the seven fluorescent reverse pairs, giving a total of 14 microarrays.
2012-04-03 | E-GEOD-34782 | biostudies-arrayexpress
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
Project description:In development, timing is of the utmost importance, and the timing of various developmental processes are often changed during evolution. We measured the timing of gene expression changes in the brains of two species of mice throughout postnatal development. Mus musculus and Mus spretus mice were bred at the MPI-EVA mouse facility. Whole brain samples were collected from mice of 3 different age classes: newborns, pups and young adults. RNA extracted from the dissected tissue was hybridized to Affymetrix MG-430 2.0 GeneChip arrays.
2009-03-09 | E-GEOD-11528 | biostudies-arrayexpress
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
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. Keywords: multi-species comparison
2006-12-13 | GSE2597 | GEO
Project description:Left cardiac ventricles and quadriceps femoris muscles were collected from young adult (16-17 wk) and early aging (86 wk) C57BL6/J mice (n=4, 2 male 2 female). Proteins were extracted in 200 µL RIPA buffer and Halt protease/phosphatase inhibitor with a hand-held sonicator followed by centrifugation, reduced with dithiothreitol, alkylated with iodoacetamide, then digested with modified sequencing grade trypsin overnight at 37degC using a filter-assisted sample preparation protocol. The peptides were fractionated using Thermo high-pH reversed phase columns into 8 fractions. Label-free bottom-up mass spectrometry was performed using data dependent acquisition on a Thermo Orbitrap Q-Exactive HF instrument using typical settings.
2021-07-23 | PXD026354 | JPOST Repository
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
Project description:Global changes in murine liver and kidney transcriptome were analyzed following different levels of malarial parasite infection.Known levels of parasites were injected in mice and transcriptomic changes were recorded with comparison to control non infected healthy mice. Two color ,Organism: Mus Musculus, Genotypic Technology designed "Custom Agilent Mus Musculus 8x15k GE Microarray (AMADID-016270) "
2012-07-31 | E-GEOD-31686 | biostudies-arrayexpress
Project description:Each array hybridization involved one male sample hybridized in competition to one female sample. For each hybridization one sample was labeled with Cy5 and the other with Cy3. Half of the male samples were labeled with Cy5 and rest with Cy3. Each hybridization was tissue-specific (i.e., hybridize male brain vs. female brain, male liver vs. female liver, etc.). A total of 10 male-female hybridizations were performed using adult brain, 7 for liver, 9 for kidney and 8 for postnatal day1 brain. One hybridization each from adult brain and liver were discarded because the hybridization intensities were far out of range.
2007-02-15 | E-MEXP-543 | biostudies-arrayexpress