Specific Lineage differentiation of proepicardial explant cultures
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE32508 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA147747
REPOSITORIES: GEO
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Project description:The HH16/17 chicken proepicardium (PE) gives rise to the embryonic epicardium (Epi) which significantly contributes formation of the coronary vasculature during cardiac development. In contrast to explanted Epi cells, explanted PE cells can undergo differentiation into a cardiac myocyte phenotype. In order to assess which genes are associated with PE differentiation into distinc cellular lineages, three interconnented microarray gene-expression time series were performed at time 0, 24, 72 and 120h after incubation with specific growth conditions: 1: Bmp2 + U0126: differentiation towards a cardiomyocyte phenotype 2: F2f2 + Vegf: differentiation towards a vascular epithelial phenotype 3: Fgf2: differentiation towards a epicardial phenotype Gene-expression profiles were determined by hybridizing Cy3 and Cy5 labelled amplified RNA to the ArkGen 20K oligo arrays in a 2-color looped experiment design, i.e., hybridization of successive time-points per array, including dye swaps, resulting in four technical replicates for each time point.
2014-01-01 | E-GEOD-32508 | biostudies-arrayexpress
Project description:The HH16/17 chicken proepicardium (PE) gives rise to the embryonic epicardium (Epi) which significantly contributes formation of the coronary vasculature during cardiac development. In contrast to explanted Epi cells, explanted PE cells can undergo differentiation into a cardiac myocyte phenotype. In order to assess which genes are associated with PE differentiation into distinc cellular lineages, two interconnented microarray gene-expression series were performed. 1: Gene-expression profiles at 12, 24, 36, 48, 60, 72 and 120 hours during cardiac myocyte differentiation from including the HH16/17 PE (t0h) were determined by hybridizing Cy3 and Cy5 labelled amplified RNA to the ArkGen 20K oligo arrays in a 2-color looped experiment design, i.e., hybridization of successive time-points per array, including dye swaps, resulting in four technical replicates for each time point. 2: Gene expression changes during normal embryonic Epi maturation were assess by hybridizing Epi from stages HH25, HH29, HH32 and HH37 in all possible pair-wise combinations, including dye-swaps, leading to 6 replicates per time point. To allow for valid comparisons between the Epi and untreated PE differentiation, these two array series were connected via hybridization of both Epi stage HH25 and HH29 with the PE explant at 48 hours in culture, with dye swaps. Keywords: time course, cardiac myocyte differentiation, embryonic coronary vessel formation, cell type comparison, mRNA expression Proepicardium to cardiac myocyte differentiation: 16 arrays for 8 time points [t0h,t12h,t24h,t36h,t48h,t60h,t72h,t120h]; successive time points hybridized per array in a loop design with dye swaps + Embryonic epicardium dfferentiation: 12 arrays for 4 time points [HH25,HH29,HH32,HH37]; all possible sample combination were hybridized with dye swaps + Epicardium to Proepicardium data connection: 4 arrays; comparing HH25 and HH29 Epicardium to t48h Proepicardium with dye swaps.
2010-12-21 | E-GEOD-13923 | biostudies-arrayexpress
Project description:The HH16/17 chicken proepicardium (PE) gives rise to the embryonic epicardium (Epi) which significantly contributes formation of the coronary vasculature during cardiac development. In contrast to explanted Epi cells, explanted PE cells can undergo differentiation into a cardiac myocyte phenotype. In order to assess which genes are associated with PE differentiation into distinc cellular lineages, two interconnented microarray gene-expression series were performed. 1: Gene-expression profiles at 12, 24, 36, 48, 60, 72 and 120 hours during cardiac myocyte differentiation from including the HH16/17 PE (t0h) were determined by hybridizing Cy3 and Cy5 labelled amplified RNA to the ArkGen 20K oligo arrays in a 2-color looped experiment design, i.e., hybridization of successive time-points per array, including dye swaps, resulting in four technical replicates for each time point. 2: Gene expression changes during normal embryonic Epi maturation were assess by hybridizing Epi from stages HH25, HH29, HH32 and HH37 in all possible pair-wise combinations, including dye-swaps, leading to 6 replicates per time point. To allow for valid comparisons between the Epi and untreated PE differentiation, these two array series were connected via hybridization of both Epi stage HH25 and HH29 with the PE explant at 48 hours in culture, with dye swaps. Keywords: time course, cardiac myocyte differentiation, embryonic coronary vessel formation, cell type comparison, mRNA expression
2010-12-21 | GSE13923 | GEO
Project description:Differentiation of totipotent embryonic cells into the first cell lineages (trophectoderm (TE) and inner cell mass (ICM), and further into epiblast (EPI) and primitive endoderm (PE)), although well studied, is only beginning to be understood at the molecular level. An in depth understanding of the regulation of these early differentiation events would enable improvements in the quality of in vitro produced embryos, as well as the study and application of bovine embryonic stem cells. The objective of this work was to perform single cell RNASeq on bovine blastocysts derived in vivo (IVV), in vitro in a conventional in vitro production system (IVC), and in vitro in reduced nutrient media (IVR). All in vitro culture was serum free. In vivo embryonic cells could be assigned based on Leiden clustering analysis, although there was some overlap in expression of marker genes. The two TE groups identified clearly separated in a uniform manifold approximation and projection (UMAP) plot from EPI groups. Putative epiblast cells could be identified. In in vitro embryos produced in a conventional system, considerable overlap in expression of marker genes made Leiden clustering difficult, but a selected count could be used for UMAP to tentatively identify one TE, 2 EPI and 2 PE groups. In assigned cell types we observed higher expression of the identifying marker genes, but some marker genes were expressed in all cell types. In IVC embryos, TE markers clustered while PE and EPI marker genes overlapped. In IVR embryos, again there was considerable overlap between marker gene expression. Like IVC embryos, TE was easily identified by clustering in IVR, but EPI and PE were too similar to distinguish. In summary, the methods used here could partially distinguish putative cell types in bovine blastocysts, although marker gene expression was not always discreet. This may not be surprising given differentiation events are in progress in the blastocyst stage embryo. TE cells were more easily distinguished than EPI and PE cells, which would support this hypothesis.
2023-09-08 | GSE215409 | GEO
Project description:Transcriptional reactivation of the paternal X chromosome occurs in specific cells of the mouse blastocyst between E(mbryonic day)3.5 and E4.5 during pre- to peri-implantation development. While the trophectoderm (TE) and the primitive endoderm (PE) maintain Xist RNA expression and thereby imprinted silencing of genes on the Xp, the epiblast (EPI) cells within the inner cell mass (ICM) gradually downregulate Xist and undergo XCR. To identify differentially expressed genes with potential roles in the XCR process, we performed single-cell expression profiling of ICM cells of blastocysts prior (E3.5, EPI Xist+), during (E4.25, EPI Xist+/Xist-) and after (E4.5, EPI Xist-) XCR. Single cell cDNAs were then assigned to cell-type of origin using qPCR for lineage-specific marker genes (epiblast: Nanog+, PE: Gata6+, TE: Cdx2+). Cells were considered of male sex if they expressed the male marker Eif2s3y or female sex in absence of Eif2s3y and presence of Xist expression in PE cells of the same embryo. Furthermore, female E4.5 epiblast cDNAs were classified according to Xist expression as before (Xist+) or after (Xist-) downregulation during XCR.
2022-11-13 | GSE208430 | GEO
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2021-10-06 | E-MTAB-10720 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10912 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10913 | biostudies-arrayexpress
Project description:In addition to their well-known role as stress-associated catecholamine hormones in animals and humans, epinephrine (EPI) and norepinephrine (NE) act as interkingdom signals between eukaryotic hosts and bacteria. However, the molecular basis of their effects on bacteria is not well understood. In initial phenotypic studies utilizing Vibrio campbellii as a model organism, we characterized the bipartite mode of action of catecholamines, which consists of promotion of growth under iron limitation, and enhanced colony expansion. In order to identify the molecular targets of the hormones, we designed and synthesized tailored probes for chemical proteomic studies. As the catechol group in EPI and NE acts as iron chelator and is prone to form a reactive quinone moiety, we devised a photoprobe based on the adrenergic agonist phenylephrine (PE), which solely influenced colony expansion on soft agar. Using this probe, we identified CheW, located at the core of the chemotaxis signaling network, as a major target. In vitro studies confirmed that EPI, NE, PE, as well as labetalol, a clinically applied antagonist, bind to purified CheW with affinity constants in the sub-micromolar range. In line with these findings, exposure of V. campbellii to these adrenergic agonists affects the chemotactic control of the bacterium. This study highlights a previously unknown effect of eukaryotic signaling molecules on bacterial motility.
2022-04-04 | PXD029119 | Pride
Project description:Mammalian embryonic development begins with the specification and segregation of the two extra-embryonic lineages, trophectoderm and primitive endoderm, from the pluripotent embryonic lineage, the epiblast. To establish a map of epiblast (EPI) versus primitive endoderm (PrE) lineage segregation which occurs within the inner cell mass (ICM), we comprehensively characterised the gene expression profiles of individual inner cells during blastocyst development. Lineage represents the two embryonic cell lineages: the epiblast (EPI), and the primitive endoderm (PE), which are segregated within the inner cell mass(ICM) during blastocyst development.
2013-11-26 | E-MTAB-1681 | biostudies-arrayexpress