Single cell expression profiles of the earliest cardiac precursor cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE63796 | GEO | 2015/10/16
SECONDARY ACCESSION(S): PRJNA269081
REPOSITORIES: GEO
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Project description:A hESC MESP1-MCHERRY reporter line was used to isolate and study the molecular character of MESP1 expressing pre-cardiac progenitors, derived from hESC. MESP1 is a key-transcription factor for pre-cardiac mesoderm and is marking the progenitor for almost all cells of the heart. This reporter line was used to study cardiac differentiation and the derivation of early cardiac progenitors in vitro.
2014-09-01 | GSE56721 | GEO
Project description:It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions. While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20M-BM-0C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce. A clonally replicated QTL mapping population (cross C94-1-2516, M-bM-^YM-^@77111 M-CM-^W M-bM-^YM-^B2388), previously characterized by Pelgas et al. (2011), was used for this study. Phenotypic data collected between 2006-2008 was used to identify extremes for time to bud set within the QTL population. Genotypes falling within the lower quartile for time to bud set for at least three of six experiments were designated as early time to bud set, while genotypes falling within the upper quartile for time to bud set for at least three of six experiments were designated as late time to bud set. Shoot tips from four ramets of each genotype were harvested for molecular analysis. Two ramets were harvested at the first sign of bud formation (Time 1) and the remaining two ramets were harvested six weeks later at which time the majority of seedlings were at the mid stage of bud set (Time 2). Microarray hybridizations were conducted to make the following comparisons: a comparison of bud development (Time 1 v. Time 2) in early time to bud set seedlings, a comparison of bud development (Time 1 v. Time 2) in late time to bud set seedlings, and a comparison of early and late time to bud set seedlings within early stages of bud formation or mid stage of bud formation. Each of two biological replicates for each time point and each phenotypic class was hybridized.
2014-09-01 | E-GEOD-57172 | biostudies-arrayexpress
Project description:It is crucial for north temperate tree species like white spruce to control timing of growth cessation and bud set in order to survive winter conditions. While much work has examined both endogenous and exogenous mechanisms influencing this transition within angiosperms, the mechanisms underlying this transition in conifers; including photoperiod perception, growth cessation and development of endodormancy, have been less well-characterized. The objective of this research was to compare the genetic responses of spruce genotypes exhibiting an early transition from active growth to bud initiation with those that delay the transition, to tease apart the molecular mechanisms underlying these complex traits. In order to gain a deeper understanding of how genomic architecture influences bud phenology and related regulatory pathways, transcript levels were quantified using a 25,045 element spruce oligonucleotide microarray. Individuals exhibiting early versus late time to bud set were selected from a large unrelated full-sib family that had been phenotyped multiple years under natural and controlled environment conditions, and harvested at an early and mid stage of bud formation. Progeny designated as early time to bud set were more likely to undergo second flush, particularly under long day (16 h) and constant temperature (20°C) conditions. Approximately 5400 genes were differentially expressed in either or both of the early and late time to bud set phenotypic classes between time points, while ca. 1500 genes were differentially expressed between phenotypic classes at either or both time points. These analyses revealed about 400 genes with putative regulatory roles. The comparison between early and late time to bud set trees revealed a large number of specifically differentially expressed genes in the early developmental stage for bud formation (957 genes, including 53 putative regulators) relative to the later developmental stage (81 genes, including 4 putative regulators). Genes implicated in the circadian cycle, photoperiodic pathway and chromatin remodeling figured prominently in these lists, providing new insight into mechanisms that may regulate bud formation in determinate species such as white spruce.
2014-09-01 | GSE57172 | GEO
Project description:A hESC MESP1-MCHERRY reporter line was used to isolate and study the molecular character of MESP1 expressing pre-cardiac progenitors, derived from hESC. MESP1 is a key-transcription factor for pre-cardiac mesoderm and is marking the progenitor for almost all cells of the heart. This reporter line was used to study cardiac differentiation and the derivation of early cardiac progenitors in vitro. hESCs were differentiated towards the cardiac lineage, expressing MESP1-mCherry at day 3 of differentiation. Total RNA obtained from isolated MESP1-mCherry expressing progenitors was compared to that of non-MESP1-expressing progenitors and undifferentiated hESCs in order to characterize MESP1-specific transcription factors and proteins.
2014-09-01 | E-GEOD-56721 | biostudies-arrayexpress
Project description:Haploinsufficiency for GATA6 is associated with congenital heart disease (CHD) with variable comorbidity of pancreatic or diaphragm defects, although the etiology of disease is not well understood. Here, we used cardiac directed differentiation from human embryonic stem cells (hESCs) as a platform to study GATA6 function during early cardiogenesis. GATA6 loss-of-function hESCs had a profound impairment in cardiac progenitor cell (CPC) specification and cardiomyocyte (CM) generation due to early defects during the mesendoderm and lateral mesoderm patterning stages. Profiling by RNA-seq and CUT&RUN identified genes of the WNT and BMP programs regulated by GATA6 during early mesoderm patterning. Furthermore, interactome analysis detected GATA6 binding with developmental transcription factors and chromatin remodelers suggesting cooperative regulation of cardiac lineage gene accessibility. We show that modulating WNT and BMP inputs during the first 48 hours of cardiac differentiation is sufficient to partially rescue CPC and CM defects in GATA6 heterozygous and homozygous mutant hESCs. This study provides evidence of the regulatory functions for GATA6 directing human precardiac mesoderm patterning during the earliest stages of cardiogenesis to further our understanding of haploinsufficiency causing CHD and the co-occurrence of cardiac and other organ defects caused by human GATA6 mutations.
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Project description:Transcriptional networks governing cardiac precursor cell (CPC) specification are incompletely understood due in part to limitations in distinguishing CPCs from non-cardiac mesoderm in early gastrulation. We leveraged detection of early cardiac lineage transgenes within a granular single cell transcriptomic time course of mouse embryos to identify emerging CPCs and describe their transcriptional profiles. Mesp1, a transiently-expressed mesodermal transcription factor (TF), is canonically described as an early regulator of cardiac specification. However, we observed perdurance of CPC transgene-expressing cells in Mesp1 mutants, albeit mis-localized, prompting us to investigate the scope of Mesp1’s role in CPC emergence and differentiation. Mesp1 mutant CPCs failed to robustly activate markers of cardiomyocyte maturity and critical cardiac TFs, yet they exhibited transcriptional profiles resembling cardiac mesoderm progressing towards cardiomyocyte fates. Single cell chromatin accessibility analysis defined a Mesp1-dependent developmental breakpoint in cardiac lineage progression at a shift from mesendoderm transcriptional networks to those necessary for cardiac patterning and morphogenesis. These results reveal Mesp1-independent aspects of early CPC specification and underscore a Mesp1-dependent regulatory landscape required for progression through cardiogenesis.
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