Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model

ABSTRACT: Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing (RNA-Seq) is a high-throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA-Seq technologies and their extensive data-analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here, we aim to perform large-scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes, which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Danio rerio

SUBMITTER: Yeliz Demirci

PROVIDER: E-MTAB-7464 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Adult zebrafish can completely regenerate their caudal fin following amputation. This complex process is initiated by the formation of an epithelial would cap over the amputation site by 12 hours post amputation (hpa). Once the cap is formed, mesenchymal cells proliferate and migrate from sites distal to the wound plane and accumulate under the epithelial cap forming the blastemal structure within 48 hpa. Blastemal cells proliferate and differentiate, replacing the amputated tissues, which are populated with angiogenic vessels and innervating nerves during the regenerative outgrowth phase which is completed around 14 days post amputation (dpa). Regenerative outgrowth does not occur in TCDD-exposed zebrafish. To identify the molecular pathways that are perturbed by TCDD exposure, male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 dpa for mRNA abundance analysis. Microarray analysis and quantitative real time PCR revealed that wound healing and regeneration alone altered the expression of nearly 900 genes by at least two fold between 1 and 5 dpa. TCDD altered the abundance of 370 genes at least two fold. Among these, several known aryl hydrocarbon responsive genes were identified in addition to several genes involved in extracellular matrix composition and metabolism. The profile of misexpressed genes is suggestive of impaired cellular differentiation and extracellular matrix composition potentially regulated by Sox9b. Experiment Overall Design: Regenerating fins were isolated at 1, 3 and 5 days post amputation. Three replicates were collected at each time point. 10 fins were pooled to comprise one replicate. Fish were dosed at 0 days post amputation with vehicle control alone or 50 ng/g TCDD. Experiment Overall Design: 1 Day Post Amputation Vehicle Exposed: GSM85187, GSM85188, and GSM85189 Experiment Overall Design: 1 Day Post Amputation TCDD Exposed: GSM85190, GSM85191, and GSM85192 Experiment Overall Design: 3 Days Post Amputation Vehicle Exposed: GSM85193, GSM85194, and GSM85195 Experiment Overall Design: 3 Day Post Amputation TCDD Exposed: GSM85196, GSM85197, and GSM85198 Experiment Overall Design: 5 Days Post Amputation Vehicle Exposed: GSM85199, GSM85200, and GSM85201 Experiment Overall Design: 5 Days Post Amputation TCDD Exposed: GSM85202, GSM85203, and GSM85204

Dataset Information

Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model

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