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Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain

ABSTRACT: Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain

PROVIDER: PRJNA824487 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18675650_1.fastq.gz	Fastqsanger.gz
	SRR18675650_2.fastq.gz	Fastqsanger.gz
	SRR18675651_1.fastq.gz	Fastqsanger.gz
	SRR18675651_2.fastq.gz	Fastqsanger.gz
	SRR18675652_1.fastq.gz	Fastqsanger.gz

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Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain

Project description:We examined uninjured and regenerating axolotl salamander retinas, including their transcriptional profile. We report that at 27 days after a retinectomy (early-mid regeneration), regenerating axolotl retinas exhibit downregulation of genes associated with neuronal networks but upregulation of genes associated with angiogenesis and the extracellular matrix. We also report differential expression of two Notch pathway effector genes, Hes1 and Hes5.

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Single-cell level transcriptomic anaylsis of the homeostatic and regenerating axolotl limb

Project description:Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, studying the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. By performing unbiased single-cell RNA-sequencing on over 25,000 cells from axolotl limbs, we identify a plethora of cellular diversity within epidermal, mesenchymal, and hematopoietic lineages in homeostatic and regenerating limbs. We identify regeneration-induced genes, develop putative trajectories for blastema cell differentiation, and propose the molecular identity and origin of fibroblast-derived blastema progenitor cells residing in homeostatic limbs. This work will enable application of molecular techniques to assess the contribution of these populations to limb regeneration. It will also facilitate work aimed at identifying transcripts and cells critical for limb regeneration.

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Project description:Here we report the results of a robust microarray experiment that examined the first 28 days of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1m of heterogeneous tissue collected from the distal limb tip. The distal 1.0mm of heterogeneous tissue from regenerating limb tip were removed and used for RNA extraction. 10 samples were collected for each of 20 time points.

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Project description:The Mexican axolotl (Ambystoma mexicanum) is one member of a select group of vertebrate animals that has retained the amazing ability to regenerate multiple body parts. In addition to being an important model system for regeneration, the axolotl is also a leading model system for developmental biologists. Many genes used in development have been identified to be reused again during regeneration, however how this molecular circuitry is controlled during regeneration is unknown. In recent years microRNAs have been identified as key regulators of gene expression during development, in many diseases and also in regeneration. Here we have used deep sequencing combined with qRT-PCR to identify microRNAs that are involved in regulating regeneration in axolotl. This approach has enabled us to identify well known families of microRNAs and in addition to identify putative novel microRNAs that differentially regulated in the regenerating tissue. These findings suggest that microRNAs may play key roles in managing the spatial and temporal expression of genes important for ensuring that the correct tissues are regenerated. small RNA Sequencing (2 samples) in Ambystoma Mexicanum

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