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Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes

PROVIDER: PRJNA754591 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15458884.fastq.gz	Fastqsanger.gz
	SRR15458885.fastq.gz	Fastqsanger.gz
	SRR15458886.fastq.gz	Fastqsanger.gz
	SRR15458887.fastq.gz	Fastqsanger.gz
	SRR15458888.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Uncut and Injured Larval Zebrafish Fin Fold Transcriptomes

Project description:We report increased expression of mitochondrial biogenesis genes in regnerating larval fin fold

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Regenerating zebrafish fin fold vs. uncut control

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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. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 Î¼g of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 Î¼g, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.

2010-05-19 | E-GEOD-11391 | biostudies-arrayexpress

Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.

Project description:Polycyclic aromatic hydrocarbons (PAHs) can alter gene expression by acting through the aryl hydrocarbon receptor (AHR). In a previous phenotypic screen of over 120 PAHs, we identified four PAHs that induce an ectopic caudal fin (called X-fin) in larval zebrafish: benzo[k]fluoranthene (BkF), dibenzo[b,k]fluoranthene, dibenzo[a,h]anthracene, and benzo[j]fluoranthene. We investigated several plausible mechanisms of X-fin formation using the most potent X-fin inducer, BkF. The X-fin phenotype was dependent on the AHR paralog Ahr2, and we performed RNA sequencing to identify altered gene expression patterns. Transcriptional profiles of distal trunk tissue, where the phenotype was manifest, were generated for animals exposed to 1% DMSO (control) or 12 μM BkF. Four time points of X-fin development were considered for transcriptomics: prior to visual emergence of X-fin (48 hpf), during manifestation of disrupted caudal fin fold development (60 and 72 hpf), and after emergence of X-fin (96 hpf).

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Transcription profiling of zebrafish larval regenerating fin tissue after exposure to TCDD in order to identify genes differentially regulated after Ahr activation

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Gender specific comparisons of gene expression during Zebrafish pectoral fin regeneration

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2011-09-02 | E-GEOD-31871 | biostudies-arrayexpress

Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.

Project description:Aryl hydrocarbon receptor mediates larval zebrafish fin duplication following exposure to benzofluoranthenes.

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Bulk RNA-seq dataset of uninjured vs injured larval zebrafish hearts at 48 hours post injury on 5 days post fertilisation

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