Mus musculus
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ABSTRACT:
PROVIDER: PRJNA259854 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression changes in limb buds of Nipbl-haploinsufficient mice
2014-09-08 | E-GEOD-60932 | ExpressionAtlas
Project description:Multiple genes are dysregulated in hindlimb buds of Nipbl-deficient embryos. In all, more than 1000 limb bud genes were found to be significantly altered in expression by microarray analysis of E10.5 mouse hindlimb buds. Small changes in expression (mostly decreases) were observed for genes involved in FGF, BMP, and SHH pathways, as well as numerous genes involved in the Wnt/planar cell polarity signaling pathway. Genes involved in the Mediator complex, Cohesin function, and Hox gene expression and functions were also dysregulated in Nipbl deficient limb buds. Microarray analysis using RNA extracted from E10.5 hindlimb limb buds harvested from stage-matched Nipbl+/- (n=12) and wildtype (n=12)
2014-08-30 | E-GEOD-60932 | biostudies-arrayexpress
Project description:Multiple genes are dysregulated in hindlimb buds of Nipbl-deficient embryos. In all, more than 1000 limb bud genes were found to be significantly altered in expression by microarray analysis of E10.5 mouse hindlimb buds. Small changes in expression (mostly decreases) were observed for genes involved in FGF, BMP, and SHH pathways, as well as numerous genes involved in the Wnt/planar cell polarity signaling pathway. Genes involved in the Mediator complex, Cohesin function, and Hox gene expression and functions were also dysregulated in Nipbl deficient limb buds.
2014-08-30 | GSE60932 | GEO
Project description:Transcriptome analysis of mouse embryonic fibroblasts of NIPBL-haploinsufficient mice
| PRJNA271694 | ENA
Project description:Congenital heart defects (CHDs) are frequently observed in the most common form of Cornelia de Lange Syndrome (CdLS), which is caused by haploinsufficiency for NIPBL, a gene involved in chromatin looping and cis-regulatory control of gene expression. Here, we surveyed cardiac defects in mice made Nipbl-haploinsufficient in the second heart field using two Cre drivers: Mef2c-Cre and Isl1-Cre. Only Isl1-Cre-driven Nipbl-haploinsufficiency resulted in CHDs – a finding we traced to the additional contribution of Isl1-haploinsufficiency caused by the Isl1-Cre allele. To test whether combined reduction of Nipbl and Isl1 cause CHDs, we made mice globally haploinsufficient for both genes. Indeed, Nipbl+/-; Isl1+/- mice exhibited a substantially higher frequency and severity of CHDs than mice haploinsufficient for either gene alone. As a member of the LIM-homeodomain transcription factor family, Isl1 is involved in chromatin looping and enhancer-promoter communication via a mechanism distinct from that of Nipbl. Nevertheless, when we performed RNA sequencing on E10.5 hearts from wildtype, Nipbl+/-, Isl1+/-, and Nipbl+/-; Isl1+/- embryos, we observed that combined haploinsufficiency resulted in largely additive gene expression changes, including dysregulation of known cardiac regulators (Irx4, Tbx1, Foxo6, Heyl, Bnc1, Sox17) and novel candidates (Gbx1, Csdc2, Myrf, Pou6f1, Zfp579, ad Zfp763). A subset of additive changes arose from opposing regulatory influences in single mutants that restored gene expression to WT levels in Nipbl⁺/⁻; Isl1⁺/⁻ hearts. For example, Hoxc4, Pitx2, Isl1 itself, and Pax6 (a known target of Isl1), were upregulated in Nipbl+/- hearts, downregulated in Isl1+/- hearts, but expressed at WT levels in Nipbl⁺/⁻; Isl1⁺/⁻ hearts. Since loss of Isl1 upregulation from Nipbl+/- to Nipbl+/-; Isl1+/- hearts coincided with a marked increase in CHDs, we propose that Isl1 upregulation compensates for the loss of cis-regulatory interactions due to Nipbl-haploinsufficiency, and protects hearts from severe CHD risk. Supporting this model, other LIM-homeodomain transcription factors (Lhx2, Lhx3, Lhx9) were also upregulated in Nipbl+/- hearts, with Lhx3 and Lhx9 showing even greater upregulation in Nipbl+/-; Isl1+/- hearts. Despite this, CHDs resulting from the combined loss of Nipbl and Isl1 were particularly severe. These findings suggest that heart development is exquisitely sensitive to small change in gene expression, leading to synergistic phenotypic interactions when relatively modest gene expression changes are combined.
2025-05-19 | GSE278563 | GEO
Project description:Cohesinopathies are characterized by mutations in the cohesin complex. Mutations in NIPBL, a cohesin loader, result in Cornelia de Lange syndrome (CdLS). CdLS is a congenital genetic disorder distinguished by craniofacial dysmorphism, abnormal upper limb development, delayed growth, severe cognitive retardation, and multiple organ malformations.It has been suggested that CdLS is caused by defects in the cohesin network that alter gene expression and genome organization. However, the precise molecular etiology of CdLS is largely unclear. To gain insights, we sequenced mRNAs isolated from mouse embryonic fibroblasts of both WT and NIPBL-haploinsufficient mice and compared their transcriptomes.
2015-10-01 | GSE64706 | GEO
Project description:m6A regulates virtually every step in RNA metabolism. However, its toles in limb development remains largely unknown. To understand the roles, we created a limb bud-specific conditional knockout (cKO) mice and control heterozygous (cHet) mice of the Mettl14 gene, which encodes an essential subunit in the m6A methyltransferase complex METTL3/METTL14. We harvested limb buds from the mice on E12.5 and applied the proteins to quantitative mass spectrometry to understand how the depletion of Mettl14 affected the proteomes.
2025-04-03 | PXD049092 | Pride
Project description:We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility.
2014-12-04 | GSE61417 | GEO
Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
| S-EPMC8784167 | biostudies-literature
Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
2004-01-02 | GSE887 | GEO