Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107377 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines
| PRJNA107063 | ENA
Project description:Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines obtained by ectopic expression of Oct4, Sox2, Klf4 and c-Myc using constitutive retroviral infection of MEFs (MCV6, MCV8, MCV8.1) or induction of lentivirus in secondary B lymphocytes obtained from iPS-derived chimeric mice (BIV8). Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison H3K4me3 and H3K27me3 ChIP-Seq in singlicate from three partially reprogrammed cell lines (BIV1, MCV8, MCV6), one iPS cell line (MCV8.1) and MEFs (subsampled from Mikkelsen et al, Nature, 2007)) Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000215
2008-05-27 | E-GEOD-11074 | biostudies-arrayexpress
Project description:Comparisons between fully and partially reprogrammed iPS cells induced by pMX-Klf4, pMX-Oct4 and pMX-Sox2 retroviruses
| PRJNA127129 | ENA
Project description:Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines obtained by ectopic expression of Oct4, Sox2, Klf4 and c-Myc using constitutive retroviral infection of MEFs (MCV6, MCV8, MCV8.1) or induction of lentivirus in secondary B lymphocytes obtained from iPS-derived chimeric mice (BIV8). Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison
2008-05-28 | GSE11074 | 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:Pluripotent stem cells have the potential to differentiate in vitro in many, if not all, functional cell types. Induced pluripotent stem cells (iPS) have recently emerged as a reproducible model of pluripotent stem cells that can be generated from post-natal tissues. To understand this process at the transcriptome level, we generated iPS cell lines, partially reprogrammed cell lines and compared their transcriptome with that of the partental human foreskin fibroblasts and human embryonic stem cell lines. Four categories of samples, comprising human foreskin fibroblasts, fully reprogrammed iPS cell lines, partially reprogrammed iPS cell lines and human embryonic stem cell lines were compared using Significance Analysis of Microarrays (SAM). These data were also compared to a compendium of differentiated human samples and a pluripotency classifier was computed.
2010-05-27 | E-GEOD-18147 | biostudies-arrayexpress
Project description:Direct Induction of Neural Progenitor Cells Transiently Passes Through a Partially-reprogrammed State
| PRJNA308807 | ENA
Project description:Induced pluripotent stem (iPS) cell reprogramming is a gradual epigenetic process that reactivates the pluripotent transcriptional network by erasing and establishing heterochromatin marks. Here, we characterize the physical structure of heterochromatin domains in full and partial mouse iPS cells by correlative Electron Spectroscopic Imaging (ESI). In somatic and partial iPS cells, constitutive heterochromatin marked by H3K9me3 is highly compartmentalized into chromocenter structures of densely packed 10 nm chromatin fibers. In contrast, chromocenter boundaries are poorly defined in pluripotent ES and full iPS cells, and are characterized by unusually dispersed 10 nm heterochromatin fibers in high Nanog-expressing cells, including pluripotent cells of the mouse blastocyst prior to differentiation. This heterochromatin reorganization accompanies retroviral silencing during conversion of partial iPS cells by Mek/Gsk3 2i inhibitor treatment. Thus, constitutive heterochromatin reorganization serves as a novel biomarker with retroviral silencing for identifying iPS cells in the very late stages of reprogramming. We compared the expression profiles of partially and fully reprogrammed iPS cell lines derived from CD1 mouse embryonic fibroblasts (MEFSs) by retroviral reprogramming (pMX-Oct4, pMX-Klf4 and pMX-Sox2). to the differentiated MEFS and the J1 embryonic stem cell line. We also studied the effect of a 2i cocktail treatment in partially reprogrammed iPS cells.
2011-09-21 | E-GEOD-21595 | biostudies-arrayexpress
Project description:Translational research is commonly performed in the C57B6/J mouse strain, chosen for its genetic homogeneity and phenotypic uniformity. Here, we evaluate the suitability of the white-footed deer mouse (Peromyscus leucopus) as a model organism for aging research, offering a comparative analysis against C57B6/J and diversity outbred (DO) Mus musculus strains. Our study includes comparisons of body composition, skeletal muscle function, and cardiovascular parameters, shedding light on potential applications and limitations of P. leucopus in aging studies. Notably, P. leucopus exhibits distinct body composition characteristics, emphasizing reduced muscle force exertion and a unique metabolism, particularly in fat mass. Cardiovascular assessments showed changes in arterial stiffness, challenging conventional assumptions and highlighting the need for a nuanced interpretation of aging-related phenotypes. Our study also highlights inherent challenges associated with maintaining and phenotyping P. leucopus cohorts. Behavioral considerations, including anxiety-induced responses during handling and phenotyping assessment, pose obstacles in acquiring meaningful data. Moreover, the unique anatomy of P. leucopus necessitates careful adaptation of protocols designed for Mus musculus. While showcasing potential benefits, further extensive analyses across broader age ranges and larger cohorts are necessary to establish the reliability of P. leucopus as a robust and translatable model for aging studies.
| S-EPMC11335981 | biostudies-literature
Project description:We compared the exactly syngeneic ntESCs and iPSCs with same genomic insertion generated from adipocyte progenitor cells (APCs) isolated from the all-iPSC mice through the primary TF mediated reprogramming by performing the high-throughput sequencing. There were 84 genes significantly upregulated in fully reprogrammed ntESCs compared with partially reprogrammed ntESCs and 391 genes upregulated in fully reprogrammed iPSCs compared with partially reprogrammed iPSCs. An overlapping gene, Grb10, was identified to associate with the pluripotency state of ntESCs.
2017-09-18 | GSE92308 | GEO