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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Methylation profiling of NimbleGen Mouse 2.1M Array

ABSTRACT: NimbleGen Mouse DNA Methylation 2.1M Array (CHARM design) was used to perform a DNA methylome analysis to unravel the molecular mechanism underlying the dedifferentiation and cell cycle reentry of mouse adult cardiomyocytes (ACMs). A total of six DNA samples (10 ng each) derived from population cells were subjected to whole genome amplification using Sigma WGA kit, and then 2.5 Âµg amplified DNA product was used for DNA methylome analysis. Three biological replicates of population ACM cells were used as controls and three biological replicates of population myocyte-derived progenitor cells (mCPCs) were used in the experimental group. Methylome microarray data using NimbleGen Mouse DNA Methylation 3x720K CpG Islands Pus RefSeq Promoter Array and DNA derived from population cells for both control cardiomyocytes and mCPCs can be found in E-MTAB-3982. Single-cell whole-transcriptome data using Affymetrix Mouse Genome 430 2.0 Array can be found in E-MTAB-3981.

ORGANISM(S): Mus musculus

SUBMITTER: Xin Chen

PROVIDER: E-MTAB-3984 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Methylation profiling of NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array

Project description:NimbleGen Mouse DNA Methylation 3x720K CpG Islands Pus RefSeq Promoter Array was used to perform a DNA methylome analysis to unravel the molecular mechanism underlying the dedifferentiation and cell cycle reentry of mouse adult cardiomyocytes (ACMs). A total of six DNA samples (10 ng each) derived from the population cells from either control adult cardiomyocytes or mCPCs were subject to whole genome amplification and then 2.5 Âµg of amplified products were used for DNA methylome analysis. There were three biological replicates in each group (both ACM controls and mCPCs). The whole genome methylome data using NimbleGen Mouse 2.1M array and genomic DNA derived from population cells for both control adult cardiomyocytes and mCPC can be found in E-MTAB-3984. Single-cell whole-transcriptome microarray data using Affymetrix Mouse Genome 430 2.0 Array can be found in E-MTAB-3981.

2016-03-22 | E-MTAB-3982 | biostudies-arrayexpress

Transcription profiling of Affymetrix Mouse Genome 430 2.0 Array

Project description:Affymetrix Mouse Genome 430 2.0 Array was used to perform single-cell transcriptome analysis to unravel the molecular mechanisms underlying the dedifferentiation and cell cycle reentry of mouse adult cardiomyocytes (ACMs). A total of six samples were used for single-cell transcriptome analysis using Affymetrix MG 430 2.0 Array coupled with a microfluidic chip for single cell isolation and NuGen Ovation Single-Cell Amplification technologies. Three biological replicates of adult cardiomyocyte single cells were used as controls and three biological replicates of myocyte-derived progenitor single cells (mCPCs) were used in the experimental group. The whole genome methylome microarray data using NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter Array and genomic DNA derived from population cells for both control adult cardiomyocytes and mCPCs can be found in E-MTAB-3982. The whole genome methylome data using NimbleGen Mouse 2.1M array and genomic DNA derived from population cells for both control adult cardiomyocytes and mCPC can be found in E-MTAB-3984.

2016-03-22 | E-MTAB-3981 | biostudies-arrayexpress

Methylomic analysis identifies the involvement of migration and adhesion genes in the ageing of primary haematopoietic stem cells

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neonatal rat cardiomyocytes stimulated by Oncostatin M

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2015-02-27 | E-MTAB-2560 | biostudies-arrayexpress

The Polycomb protein Pcgf2/Mel18 regulates mesoderm cell fate-specification of embryonic stem cells through multiple mechanisms

Project description:Polycomb complexes are essential regulators of stem cell identity, yet very little is known about their molecular mechanisms during cell differentiation. Pcgf proteins (Pcgf1/2/3/4/5/6) are core subunits of the Polycomb repressive complex 1 (PRC1). It has been recently proposed that specific Pcgf proteins are associated to particular PRC1 complexes, yet the molecular and biological functions of different Pcgf proteins remains largely elusive. Using specific differentiation protocols, we have elucidated a role for Pcgf2/Mel18 in specifically regulating mesoderm differentiation. Mechanistically, during early cardiac mesoderm differentiation, Pcgf2/Mel18 functions as a classical Polycomb protein by repressing pluripotency, lineage specification, late cardiac differentiation and negative regulators of the BMP pathway, yet Pcgf2/Mel18 also positively regulates the expression of key mesoderm transcription factors, revealing a novel function of Pcgf2/Mel18 in gene activation during cardiac differentiation. Mel18 depletion results in an unbalance of pathways that positively and negatively regulate cardiac differentiation. We propose that Mel18 is a novel epigenetic factor that controls mesoderm differentiation by opposing molecular mechanisms. List of ChIPseq samples: Mel18 in ESCs and MES, Ring1b, RYBP and Cbx2 in MES, IgG in MESs. List of RNAseq experiments: Mel18 KD, Ring1b KO and CTR in ESCs, Mel18 KD and CTR in MES, Mel18 KD and CTR in CMs.

2015-09-04 | E-GEOD-67868 | biostudies-arrayexpress

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Gene expression profiling of wildtype vs. transgenic mice expressing the cardiac specific genetically encoded FRET biosensor Epac1-PLN

Project description:3’,5’-cyclic adenosine monophosphate (cAMP) is an ubiquitous second messenger which regulates multiple physiological functions by acting in distinct subcellular microdomains. Although several targeted cAMP biosensors have been developed and used in cell lines or neonatal cardiomyocytes, it is unclear whether such biosensors can be successfully used in vivo, especially in the context of disease. Here, we generated the first transgenic mouse model expressing a targeted cAMP sensor (Epac1-PLN) and analyzed microdomain-specific second messenger dynamics in the vicinity of the sarcoplasmic reticulum calcium ATPase (SERCA). We demonstrate the biocompatibility of this targeted sensor and its potential for real-time monitoring of compartmentalized cAMP signaling in adult cardiomyocytes isolated from healthy mouse heart and from in vivo cardiac disease model. Finally, we used gene arrays to verify that the mRNA expression levels of the main players involved in cAMP signaling such as beta-ARs, G-protein, adenylyl cyclases, PKAs, PDEs, and Epac were not significantly changed between wildtype and transgenic Epac1-PLN expressing cardiomyocytes. To compare cardiac specific mRNA expression between wildtype and Epac1-PLN transgenic mice, cardiomyocyte RNA from total of 5 individual wildtype and 5 Epac1-PLN transgenic mice was isolated and submitted for the Illumina gene array analysis to the Göttingen transcriptome analysis laboratory (TAL).

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