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Single-cell RNA-seq achieve the transcriptome module the SAN morphogenesis and the pacemaking cell fate determinant

ABSTRACT: We analyze three (WT, Shox2-KO, Double-KO) different samples to segregate the transcriptional factors that modulate the SAN morphogenesis and the pacemaking cell fate determinants.

ORGANISM(S): Mus musculus

PROVIDER: GSE143997 | GEO | 2020/05/20

REPOSITORIES: GEO

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Single-cell RNA-seq achieve the transcriptome module the SAN morphogenesis and the pacemaking cell fate determinant

Project description:Single-cell RNA-seq achieve the transcriptome module the SAN morphogenesis and the pacemaking cell fate determinant

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Expression data from SAN tissue of WT and HCN4FEA mice

Project description:HCN4 channels are the major HCN channel isoform expressed in the sinoatrial node (SAN) and play a key role in cardiac pacemaking. We have characterized the gene expression profile in the SAN of adult mice expressing cAMP-insensitive HCN4 channels (HCN4FEA mice) in comparison to WT mice. In this dataset, we include the expression data obtained from dissected mouse SAN tissue of WT and HCN4FEA mice. These data are used to show that there are no relevant compensatory up- oder down-regulated genes in the SAN of HCN4FEA mice.

2020-09-11 | GSE138086 | GEO

Expression data from Shox2 knockout and wildtype right atria of E11.5 mouse hearts

Project description:The heart’s rhythm is initiated and regulated by a group of specialized cells in the sinoatrial node (SAN), the primary pacemaker of the heart. Abnormalities in the development of the SAN can result in irregular heart rates (arrhythmias). Although several of the critical genes important for SAN formation have been identified, our understanding of the transcriptional network controlling SAN development remains at a relatively early stage. The homeodomain transcription factor Shox2 plays an essential early role in the specification and patterning of the SAN. Here, we compared gene expression levels in the right atria of wildtype and Shox2-/- hearts using microarray experiments to identify Shox2 target genes.

2013-06-03 | GSE39924 | GEO

Expression data from Shox2 knockout and wildtype right atria of E11.5 mouse hearts

Project description:The heartM-bM-^@M-^Ys rhythm is initiated and regulated by a group of specialized cells in the sinoatrial node (SAN), the primary pacemaker of the heart. Abnormalities in the development of the SAN can result in irregular heart rates (arrhythmias). Although several of the critical genes important for SAN formation have been identified, our understanding of the transcriptional network controlling SAN development remains at a relatively early stage. The homeodomain transcription factor Shox2 plays an essential early role in the specification and patterning of the SAN. Here, we compared gene expression levels in the right atria of wildtype and Shox2-/- hearts using microarray experiments to identify Shox2 target genes. Right atria of E11.5 mouse embryos were dissected and genotyped for RNA extraction. RNA from 6 embryos and 2 independent pregnancies was pooled per genotype (Wildtype and Shox2 Knockout) and compared.

2013-06-03 | E-GEOD-39924 | biostudies-arrayexpress

SNP genotyping of ǂKhomani San

Project description:48 ǂKhomani San living in the South African Kalahari were genotyped using the Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays

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MiRNAs sequence of macrophages derived exosoms in WT group and Roquin-1 san:san group.

Project description:We reported the function of Roquin-1 in the miRNA-sorting of macrophages derived exosomes. At first, we used the supernatant of 929 cells to culture the bone marrow derived macrophages (BMDM) from bone marrow cells of WT and Roquin-1 san:san mice. Then, we isolated the macrophages derived exosomes by ultracentrifugation. At last, we performed Next-generation sequencing to detect the differences of miRNA-sorting between WT and Roquin-1 macrophages derived exosomes.

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Genome-wide chromatin-immunoprecipitation studies of purified SAN cells reveals critical direct targets of ISL1 and suggests potential co-factor families for ISL1 action in SAN cells

Project description:Understanding factors that drive development and function of the sinoatrial node (SAN) is crucial to development of potential therapies for sinus arrhythmias, including potential generation of biological pacemakers. Here, we identify a key cell autonomous role for the LIM homeodomain transcription factor ISL1 for survival, proliferation and function of pacemaker cells throughout development. Chromatin immunoprecipitation assays performed utilizing antibody to ISL1 in chromatin extracts from FACS purified SAN cells demonstrated that ISL1 directly binds genomic regions within several genes critical for normal pacemaker function, including subunits of the L-type calcium channel, Ank2, and Tbx3. Other genes implicated in abnormal heart rhythm in humans were also direct downstream targets of ISL1 in SAN cells. Our studies represent the first in vivo ChIP-seq studies for SAN cells which provide a basis for further exploration of factors critical to SAN formation and function and highlight the potential for utilization of ISL1 in combination with other SAN transcription factors for generating pacemaker cells for therapy or drug screening purposes.

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Genome-wide DNA methylation of ǂKhomani San

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Odz4 upregulates SAN-specific genes to promote differentiation into cardiac pacemaker-like cells

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2024-07-07 | GSE271665 | GEO

Cadmium specific proteomic responses of Pseudomonas aeruginosa san ai

Project description:Pseudomonas aeruginosa san ai resists a high concentration of up to 7.2 mM of cadmium. Leaving biomass of P. aeruginosa san ai exposed to sub-lethal concentration of cadmium (0.9 mM) adsorbed 75% of added cadmium after 48 hours, while remaining 25% in culture supernatant was adsorbed by exopollysaccaryde, implying a large biosorption potential of leaving biomass and its exopollysaccaryde. Inner cell response on the protein level was investigated by shotgun proteomics approach based on liquid chromatography and tandem mass spectrometry coupled with bioinformatics to identify proteins in complex protein fractions obtained by size exclusion chromatography used to preserve native forms of metalloproteins and protein complexes. Using this approach a total of 59 proteins were observed as up-regulated in cadmium- amended culture. Almost a third of the total number of up-regulated were metalloproteins. P. aeruginosa san ai developed a complex mechanism to adapt to cadmium, based on: extracellular biosorption, bioaccumulation, the formation of biofilm, controlled siderophore production, enhanced respiration and modified protein profile. An increased abundance of proteins involved in cell energy metabolism, amino acid metabolism, cell motility and posttranslational modifications, primarily based on thiol-disulfide exchange, were observed. Enhanced oxygen consumption of biomass in cadmium- amended culture versus control was found. Our results signify that P. aeruginosa san ai has a great potential for application in bioremediation of cadmium polluted sites.

2022-05-19 | PXD008020 | Pride

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