The effects of different types of sugars on vascular cell diffentiation in a tissue culture system, VISUAL
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PROVIDER: PRJNA925524 | ENA |
REPOSITORIES: ENA
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Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To investigate the effects of differenet sugars in VISUAL, we performed GeneChip analysis .
2023-05-16 | GSE223284 | GEO
Project description:We have previously established an in vitro tissue culture system (named VISUAL; Kondo et al., 2016), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and bes1 during vascular development, we performed GeneChip analysis using VISUAL.
2018-02-07 | GSE110199 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To compare gene expression profiles between WT and apl during vascular development, we performed GeneChip analysis using VISUAL.
2016-05-25 | GSE80026 | GEO
Project description:Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus- specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.
2022-09-04 | GSE212528 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL-CC), in which phloem companion cell (CC) differentiation can be induced with Arabidopsis thaliana cotyledons. To compare gene expression profiles between VISUAL and VISUAL-CC, we conducted GeneChip analysis using two different in vitro cultures. CC-S means a sample that strongly induces CC differentiation. CC-M means a sample that moderately induces CC differentiation. V means a VISUAL sample, that does not induce CC differentiation at all.
2020-03-31 | GSE141037 | GEO
Project description:We established a novel in vitro tissue culture system (named VISUAL), in which xylem and phloem differentiation can be induced with Arabidopsis thaliana cotyledons To isolate phloem-specific genes in VISUAL, we performed GeneChip analysis after cell-sorting experiments with SEOR1pro::SEOR1-YFP.
2016-05-25 | GSE80027 | GEO
Project description:The evolution of visual systems is tightly linked to the diversification of visually guided behaviors. Heliconius butterflies, renowned for their diverse wing color patterns and complex visual behaviors such as mate choice, provide an ideal system to study this process. Here, we investigate the evolution of compound eye cell types and their association with visual behavioral loci across species spanning a complete speciation continuum, from a polymorphic population to reproductively isolated species. By integrating population genomics, chromatin conformation capture, and single-cell transcriptomics, we uncover the multi-modal mechanisms driving visual system evolution. Within a single population polymorphic for mate preference, we characterize the cis-regulatory landscape of a 1 Mb mate preference locus and identify senseless-2 as a glia-expressing candidate preference gene. Extending to cross-species comparisons, we demonstrate that visual system evolution is shaped not only by transcriptomic divergence but also by cellular compositional shifts. Furthermore, we reveal that photoreceptors, particularly the color-sensing R7, exhibit significantly accelerated rates of gene expression evolution compared to downstream neurons and glia. Indeed, we characterize novel R2/5 and R7 photoreceptor subtypes, showing that cellular subfunctionalization can arise through the co-option of existing gene regulatory networks. Together, our comparative single-cell analysis of compound eyes across multiple species provides a unifying framework that bridges microevolutionary transcriptomic divergence with macroevolutionary cellular innovations.
2026-09-24 | GSE330347 | GEO
Project description:The evolution of visual systems is tightly linked to the diversification of visually guided behaviors. Heliconius butterflies, renowned for their diverse wing color patterns and complex visual behaviors such as mate choice, provide an ideal system to study this process. Here, we investigate the evolution of compound eye cell types and their association with visual behavioral loci across species spanning a complete speciation continuum, from a polymorphic population to reproductively isolated species. By integrating population genomics, chromatin conformation capture, and single-cell transcriptomics, we uncover the multi-modal mechanisms driving visual system evolution. Within a single population polymorphic for mate preference, we characterize the cis-regulatory landscape of a 1 Mb mate preference locus and identify senseless-2 as a glia-expressing candidate preference gene. Extending to cross-species comparisons, we demonstrate that visual system evolution is shaped not only by transcriptomic divergence but also by cellular compositional shifts. Furthermore, we reveal that photoreceptors, particularly the color-sensing R7, exhibit significantly accelerated rates of gene expression evolution compared to downstream neurons and glia. Indeed, we characterize novel R2/5 and R7 photoreceptor subtypes, showing that cellular subfunctionalization can arise through the co-option of existing gene regulatory networks. Together, our comparative single-cell analysis of compound eyes across multiple species provides a unifying framework that bridges microevolutionary transcriptomic divergence with macroevolutionary cellular innovations.
2026-09-24 | GSE330237 | GEO
Project description:Mapping Visual Functions onto Molecular Cell Types in the Mouse Superior Colliculus
| PRJNA925147 | ENA
Project description:The evolution of visual systems is tightly linked to the diversification of visually guided behaviors. Heliconius butterflies, renowned for their diverse wing color patterns and complex visual behaviors such as mate choice, provide an ideal system to study this process. Here, we investigate the evolution of compound eye cell types and their association with visual behavioral loci across species spanning a complete speciation continuum, from a polymorphic population to reproductively isolated species. By integrating population genomics, chromatin conformation capture, and single-cell transcriptomics, we uncover the multi-modal mechanisms driving visual system evolution. Within a single population polymorphic for mate preference, we characterize the cis-regulatory landscape of a 1 Mb mate preference locus and identify senseless-2 as a glia-expressing candidate preference gene. Extending to cross-species comparisons, we demonstrate that visual system evolution is shaped not only by transcriptomic divergence but also by cellular compositional shifts. Furthermore, we reveal that photoreceptors, particularly the color-sensing R7, exhibit significantly accelerated rates of gene expression evolution compared to downstream neurons and glia. Indeed, we characterize novel R2/5 and R7 photoreceptor subtypes, showing that cellular subfunctionalization can arise through the co-option of existing gene regulatory networks. Together, our comparative single-cell analysis of compound eyes across multiple species provides a unifying framework that bridges microevolutionary transcriptomic divergence with macroevolutionary cellular innovations.
2026-09-24 | GSE330236 | GEO