Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA189668 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype. Reduced representation bisulfite sequencing of 4 mouse chromaffin cell samples (2 Sdhb wild-type and 2 Sdhb knock-out).
2013-05-06 | E-GEOD-44350 | biostudies-arrayexpress
Project description:We report the analysis of DNA methylation in mouse chromaffin cell lines using reduced representation bisulfite sequencing (RRBS). We compared DNA methylation profiles of cell lines with or without a knock-out of Sdhb gene, showing that Sdhb disruption results in a hypermethylator phenotype.
2013-05-06 | GSE44350 | GEO
Project description:Pheochromocytoma (PCC) and paraganglioma (PGL) are neuroendocrine tumours arising in the adrenal medulla and paraganglia of the autonomous nervous system, respectively. Malignant PCC/PGL are mostly caused by germline mutations of SDHB, encoding a subunit of succinate dehydrogenase. Gene expression changes associated with SDHB inactivation were investigated in a two genetically defined murine cellular models. These models were generated by Cre-mediated recombination in spontaneously immortalized mouse chromaffin cells (imCCs) and adrenal fibroblasts (MAFs).
2015-11-04 | E-MTAB-3403 | biostudies-arrayexpress
Project description:Dysregulated extravillous trophoblast invasion and proliferation are known to increase the risk of recurrent spontaneous abortion (RSA); however, the underlying mechanism remains unclear. Herein, in our retrospective observational case-control study we show that villous samples from RSA patients, compared to healthy controls, display reduced succinate dehydrogenase complex iron sulfur subunit (SDHB) DNA methylation, elevated SDHB expression, and reduced succinate levels, indicating that low succinate levels correlate with RSA. Moreover, we find high succinate levels in early pregnant women are correlated with successful embryo implantation. SDHB promoter methylation recruited MBD1 and excluded c-Fos, inactivating SDHB expression and causing intracellular succinate accumulation which mimicked hypoxia in extravillous trophoblasts cell lines JEG3 and HTR8 via the PHD2-VHL-HIF-1α pathway; however, low succinate levels reversed this effect and increased the risk of abortion in mouse model. This study reveals that abnormal metabolite levels inhibit extravillous trophoblast function and highlights an approach for RSA intervention.
2021-10-06 | MTBLS2148 | MetaboLights
Project description:Genome wide DNA methylation profiling of thymocytes from wild type and Nsd2 knock out (KO) and Nsd2 knock in (KI). The 906th Proline of Nsd2 was substituted to Leucine in Nsd2 KI by gene editing. The Illumina Infinium Mouse methylation Beadchip was used to obtain DNA methylation profiles across approximately 270,000 CpGs in thymocytes. Samples included 2 wild type, 2 heterozygous knock out, 1 heterozygous knock in, and 1 homozygous knock in.
2024-04-01 | GSE221621 | GEO
Project description:The effect of PACAP treatment on the bovine chromaffin cells in vitro were investigated using mouse Mm36kd3 arrays. Although chromaffin cells have indigenous PACAP, the experiment was designed to find out the effect of additional PACAP on additional activation or suppression of transcription. Keywords: compound treatment design cy5 labelled RNA from PACAP treated bovine chromaffin cells were paired with cy3 labelled RNA from control chromaffin cells for hybridization. Four biological repeats were carried out.
2010-05-26 | E-GEOD-7406 | biostudies-arrayexpress
Project description:Despite the massive research efforts of the post-genomics era, a significant fraction of genes remain without functional annotation. Proteomics holds the promise to close significant gaps, but has only recently reached the scalability and precision of genome-scale studies. Here we combine large-scale proteomics with functional genomics and use a streamlined platform for fast yeast proteomics to record quantitative proteomes of ~4,500 single knock-out strains of a genome-scale yeast knock-out collection.
2022-08-15 | MSV000090136 | MassIVE
Project description:The effect of PACAP treatment on the bovine chromaffin cells in vitro were investigated using mouse Mm36kd3 arrays. Although chromaffin cells have indigenous PACAP, the experiment was designed to find out the effect of additional PACAP on additional activation or suppression of transcription. Keywords: compound treatment design
2008-03-01 | GSE7406 | GEO
Project description:DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and to date no base-resolution maps exist to support and refine it. Here, we generated genome-scale DNA methylation maps in mouse gametes and through post-implantation embryogenesis. We find that the oocyte already exhibits global hypomethylation, most prominently at specific subfamilies of LINE-1 and LTR-containing retro-elements, which are disparate between gametes and resolve to lower methylation values in zygote. Surprisingly, the oocyte contributes a unique set of Differentially Methylated Regions (DMRs), including many CpG Island promoter regions, that are maintained in the early embryo but are lost at the onset of embryonic specification and absent in somatic cells. In contrast, sperm contributed methylation includes retrotransposons that become completely methylated after the blastocyst stage. Our data provide a complete genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic and before returning to the canonical somatic pattern. Comparison of DNA methylation patterns in mouse gametes and through embryogenesis using Reduced Representation Bisulfite Sequencing (RRBS)
2012-03-28 | E-GEOD-34864 | biostudies-arrayexpress
Project description:In this study, we mapped modification of lysine 4 and lysine 27 of histone H3 genome-wide in a series of mouse embryonic stem cells (mESCs) varying in DNA methylation levels based on knock-out and reconstitution of DNA methyltransferases (DNMTs). We extend previous studies showing cross-talk between DNA methylation and histone modifications by examining a breadth of histone modifications, causal relationships, and direct effects. Our data shows a causal regulation of H3K27me3 at gene promoters as well as H3K27ac and H3K27me3 at tissue-specific enhancers. We also identify isoform differences between DNMT family members. This study provides a comprehensive resource for the study of the complex interplay between DNA methylation and histone modification landscape. RNA-seq performed on wild-type, Dnmt triple knock-out (Dnmt1/3a/3b; TKO), Dnmt double knock-out (Dnmt3a/3b; DKO), and respective reconstitution mouse embryonic stem cell lines
2016-08-02 | E-GEOD-77003 | biostudies-arrayexpress