Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae
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ABSTRACT:
PROVIDER: PRJNA666695 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12749700.fastq.gz | Fastqsanger.gz | |||
| SRR12749697.fastq.gz | Fastqsanger.gz | |||
| SRR12749698.fastq.gz | Fastqsanger.gz | |||
| SRR12749699.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.
2021-07-17 | GSE158851 | GEO
Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae.
2014-07-17 | GSE44395 | GEO
Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae. Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.
2014-07-17 | E-GEOD-44395 | biostudies-arrayexpress
Project description:Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.
2019-08-13 | GSE112498 | GEO
Project description:Aim: In this study, we aim to establish a diabetic zebrafish model and examine the effects of high glucose on inflammation and tissue regeneration. Materials and Methods: Tübingen strain zebrafish (wild type, WT), Tg (mpo: EGFP), and Tg (coro1a: EGFP) zebrafish were employed. Caudal fin amputation was performed to study tissue regeneration and inflammation. Results: Our results showed that high glucose increased the recruitment of neutrophils and macrophages after amputation. Most importantly, limb regeneration was severely impaired after amputation in zebrafish larvae exposed to 222 mM glucose for 14 days. In addition, inflammatory factors IL-1β, IL-6, TNF-α, VCAM-1, and MCP-1, which are closely related to the development of diabetic wound, increased significantly in caudal fin amputation after glucose exposure. The p38 inhibitor SB203580 can reduce the expression of inflammatory factors and promote regeneration in high glucose. It showed that caudal fin amputation after glucose exposure resulted in genes enrichment of several pathways involved in amino acid metabolism, lipid metabolism, and inflammation based on high-throughput transcriptome sequencing. Conclusions: Overall, this experimental system using zebrafish larvae provides a wide spectrum of genetic and molecular profile recapitulating human diabetes which will be beneficial for basic research of inflammation and regeneration in diabetic background and promote translational research for diabetes therapy.
2025-09-01 | GSE260718 | GEO
Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing.
2016-06-01 | GSE74415 | GEO
Project description:Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors. MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs. Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration. We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing. The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing. Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.
2016-06-01 | E-GEOD-74415 | biostudies-arrayexpress
Project description:Using Agilent custom made expression microarrays we analyzed the difference of gene expression in caudal fin tissues of wild type fish and transgenic fish that can form melanomas. For this we used a transgenic line with forced expression of V600EBRAF that resulted in melanocyte hyperplasia, while expression of G12VHRAS resulted in malignant melanocyte neoplasia that initially grows radially (RGP) and then vertically (VGP) This microarray study was designed to determine the gene expression profile of zebrafish caudal fins in wild type or transgenic animals. Total RNA extracted from 3 pools of 10 caudal fins were used for WT, BRAF and RGP samples, whilst for VGP RNA was extracted from 3 pools of 6 caudal fin tumours.
2016-01-13 | E-GEOD-76791 | biostudies-arrayexpress
Project description:Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated. Caudal fin tissue at 2dpf and regenerating fins were isolated at 1, 2and 3 days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.
2008-04-07 | E-GEOD-10188 | biostudies-arrayexpress
Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response.
2008-10-01 | GSE11391 | GEO