Transcriptome analysis of axolotl oropharyngeal explants during taste bud differentiation stages

Kohli, Priya; Marazzi, Lauren; Eastman, Deborah

doi:10.1016/j.mod.2020.103597

Cited by 3 publications

(3 citation statements)

References 60 publications

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“…The current difficulties in the study of non-canonical organ regeneration in salamanders are mainly due to: (1) The small number of researchers; (2) The lack of technical means for the study; and (3) The lack of background and resources for the study. Recent progress in embryo, tissue and cell transplantation [58,[64][65][66][67][68][69], virusmediated cell labeling [70,71], transgenic [72][73][74][75][76][77][78][79], tissue clearing [80][81][82][83] and live imaging [77,[83][84][85][86], gene editing [87][88][89][90], de novo sequencing [88,[91][92][93][94][95][96][97], singlecell [7,[98][99][100][101][102][103][104]…”

Section: Discussionmentioning

confidence: 99%

“…The current difficulties in the study of non‐canonical organ regeneration in salamanders are mainly due to: (1) The small number of researchers; (2) The lack of technical means for the study; and (3) The lack of background and resources for the study. Recent progress in embryo, tissue and cell transplantation [58, 64–69], virus‐mediated cell labeling [70, 71], transgenic [72–79], tissue clearing [80–83] and live imaging [77, 83–86], gene editing [87–90], de novo sequencing [88, 91–97], single‐cell [7, 98–105] and spatiotemporal [7, 103–107] multi‐omics technologies (Figure 2) have dramatically expanded knowledge about embryonic and tissue development, and the evolution of animal behavior and have advanced human understanding of the spatiotemporal dynamics of cells and genes at the genetic, transcriptional, and protein levels during the regeneration of canonical organs in salamanders, and their regulation of regeneration. Currently, models of pneumonectomy, hepatectomy, nephrectomy, and renal drug injury have been successfully constructed in salamanders, based on which we have discovered the regenerative potential of salamander alveolar epithelial cells, hepatocytes, and other cells and structures such as the alveoli, glomeruli, and renal tubules.…”

Section: Discussionmentioning

confidence: 99%

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Salamanders aid research into mechanisms of non‐canonical organ regeneration for clinical applications

Yin,

Cui,

Liu

et al. 2024

Medicine Advances

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Salamanders possess remarkable regenerative capacities for organ regeneration among tetrapod vertebrates. Previous research has primarily focused on studying the regeneration of canonical tissues or organs such as limbs, tail, brain, spinal cord, heart, and lens. The advancements made in these areas have broader implications for understanding regeneration and developing therapeutic approaches for these organs, not only in salamanders but also in other vertebrates. In recent years, there has been an increasing interest in studying the regeneration of non‐canonical organs in salamanders, such as the liver, lungs, kidneys, and pancreas. This diversification of research has opened up new avenues and provided potential solutions to challenging clinical problems. This review aims to summarize the progress made in the field of non‐canonical organ regeneration in salamanders and provides an outlook on future research directions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Salamanders aid research into mechanisms of non‐canonical organ regeneration for clinical applications

Yin,

Cui,

Liu

et al. 2024

Medicine Advances

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“…Embryos were incubated in 20% Holtfreter's solution at 22°C and staged according to Bordzilovskaya et al. [1] . Isolation and culturing of oropharyngeal endodermal explants (OPEs) from stage 15 embryos was performed as described by Parker et al.…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants

2020

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Animal nutrition and toxin deterrence rely on the ability to taste, which occurs through columnar taste cells clustered within taste buds. Taste buds in mammals are located within specialized tissues, called papillae. However, taste buds in fish and amphibians, such as axolotls ( Ambystoma mexicanum ), are not housed in papillae, rather they are embedded within the pharyngeal epithelium. This simplified tissue level organization, along with the ability of cultured oropharyngeal explants from early embryos to produce taste buds on the same time-line as embryos, make the axolotl an excellent model to identify molecules specifically involved in taste bud cell differentiation. We performed de novo transcriptomic analysis on RNA sequences from three different stages of oropharyngeal explants: stages 37/38, 39, and 41. RNA-seq data from 17 total samples representing these stages were pooled to generate a de novo assembly of the transcriptome using a Trinity pipeline. From 27.9Gb of raw sequences, we identified 21,244 transcripts. To our knowledge, this is the first published assembly of axolotl oropharyngeal endoderm explants. This data and transcriptome assembly relate to the research article “Transcriptome Analysis of Axolotl Oropharyngeal Explants During Taste Bud Differentiation Stages” (Kohli et al. 2020). This RNA-seq data and transcriptome assembly provide information on genes expressed in the oropharyngeal endoderm and will be valuable in the identification of taste bud development genes.

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Transcriptome analyses reveal differentially expressed genes associated with development of the palatal organ in bighead carp (Hypophthalmichthys nobilis)

Wang

Chen

et al. 2023

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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Transcriptome analysis of axolotl oropharyngeal explants during taste bud differentiation stages

Cited by 3 publications

References 60 publications

Salamanders aid research into mechanisms of non‐canonical organ regeneration for clinical applications

Salamanders aid research into mechanisms of non‐canonical organ regeneration for clinical applications

Transcriptome dataset for RNA-seq analysis of axolotl embryonic oropharyngeal endoderm explants

Transcriptome analyses reveal differentially expressed genes associated with development of the palatal organ in bighead carp (Hypophthalmichthys nobilis)

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