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Beadchip technology to detect DNA methylation in the mouse faithfully recapitulates whole genome bisulfite sequencing

ABSTRACT: Beadchip technology to detect DNA methylation in the mouse faithfully recapitulates whole genome bisulfite sequencing

PROVIDER: PRJNA950435 | ENA |

REPOSITORIES: ENA

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Beadchip technology to detect DNA methylation in mouse faithfully recapitulates whole-genome bisulfite sequencing.

Project description:Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3-99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.

| S-EPMC10131490 | biostudies-literature

Beadchip technology to detect DNA methylation in the mouse faithfully recapitulates whole genome bisulfite sequencing

Project description:DNA methylation data generated by the Illumina Mouse Methylation Beadchip for comparison to WGBS

2023-05-12 | GSE228602 | GEO

Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas

Project description:Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas

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Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [Illumina Array]

Project description:Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [Illumina Array]

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Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [RNA-Seq]

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Generation of NPM1-ALK translocation in human T lymphocytes faithfully recapitulates the diversity of ALK+ ALCL tumor phenotype

Project description:Generation of NPM1-ALK translocation in human T lymphocytes faithfully recapitulates the diversity of ALK+ ALCL tumor phenotype

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A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks.

Project description:Dominant gain-of-function alleles of Arabidopsis phytochrome B were recently shown to confer light-independent, constitutive photomorphogenic (cop) phenotypes to transgenic plants (Su and Lagarias, 2007). In the present study, comparative transcription profiling experiments were performed to assess whether the pattern of gene expression regulated by these alleles accurately reflects the process of photomorphogenesis in wild-type Arabidopsis. Whole-genome transcription profiles of dark-grown phyAphyB seedlings expressing the Y276H mutant of phyB (YHB) revealed that YHB reprograms about 13% of the Arabidopsis transcriptome in a light-independent manner. The YHB-regulated transcriptome proved qualitatively similar to but quantitatively greater than those of wild-type seedlings grown under 15 or 50 micromol m(-2) m(-1) continuous red light (Rc). Among the 2977 genes statistically significant two-fold (SSTF) regulated by YHB in the absence of light include those encoding components of the photosynthetic apparatus, tetrapyrrole/pigment biosynthetic pathways, and early light-responsive signaling factors. Approximately 80% of genes SSTF regulated by Rc were also YHB-regulated. Expression of a notable subset of 346 YHB-regulated genes proved to be strongly attenuated by Rc, indicating compensating regulation by phyC-E and/or other Rc-dependent processes. Since the majority of these 346 genes are regulated by the circadian clock, these results suggest that phyA- and phyB-independent light signaling pathway(s) strongly influence clock output. Together with the unique plastid morphology of dark-grown YHB seedlings, these analyses indicate that the YHB mutant induces constitutive photomorphogenesis via faithful reconstruction of phyB signaling pathways in a light-independent fashion.

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Somatic muscle engineering faithfully recapitulates a molecular spectrum of high-risk sarcomas [Illumina Array]

Project description:A particular challenge hampering therapeutic advancements for high-risk sarcoma patients is the broad spectrum of molecularly distinct sarcoma entities and the corresponding lack of suitable model systems to recapitulate and study these diseases. To overcome this predicament, we developed a novel genetically-controlled, yet versatile mouse modeling platform allowing delivery of different genetic lesions by electroporation (EPO) of the thigh muscle in wildtype mice. This sarcoma EPO-GEMM (EPO-based genetically engineered mouse model) platform allowed the generation of ten biologically distinct sarcoma entities and subtypes on an isogenic background, including the first model of ETV6::NTRK3-driven infantile fibrosarcoma and of BCOR-inactivated rhabdomyosarcoma. Comprehensive histological and molecular profiling revealed that this mouse sarcoma cohort recapitulates the molecular diversity observed across the human disease with gene fusion and Trp53 status acting as major determinants of sarcoma biology. Integrative cross-species analyses confirmed faithful recapitulation of the human disease, including the expression of relevant immunotherapy targets.

2025-04-11 | GSE265873 | GEO