ScRNA-seq of fin and body zebrafish melanocytes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA753151 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15390205_1.fastq.gz | Fastqsanger.gz | |||
| SRR15390205_2.fastq.gz | Fastqsanger.gz | |||
| SRR15390206_1.fastq.gz | Fastqsanger.gz | |||
| SRR15390206_2.fastq.gz | Fastqsanger.gz | |||
| SRR15390207_1.fastq.gz | Fastqsanger.gz |
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Project description:Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: (1) cell lineage: melanocyte vs bulk microenvironment, (2) anatomic location: fin vs body, (3) genotype: wildtype vs CRKL,GAB2,TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL.
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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.
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