Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Bulk RNAseq of caudal fin regeneration in 24 hours post-amputation blastemas from zebrafish treated with the bioactive extract of the microalga Skeletonema costatum.

ABSTRACT: Adult Zebrafish (Danio rerio, 3 months old) were subjected to caudal fin amputation and exposed for 24 hours to either the ethanolic extract from the microalga Skeletonema costatum or its vehicle (ethanol 0.1 %) via waterborne exposure. At 24 hours post-amputation, fish were sacrificed. Regenerated blastemas were dissected and 10 blastemas were pooled in a 1.5 mL tube (5 tubes/replicates) per experimental condition.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Danio rerio

SUBMITTER: Alessio Carletti

PROVIDER: E-MTAB-14677 | 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

Bulk RNAseq of caudal fin regeneration in 24 hours post-amputation blastemas from zebrafish treated with the bioactive extract of the microalga Skeletonema costatum.

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