{"database": "metadata", "table": "run_metadata", "rows": [[10358, "ERR7720649", "ERX7289613", "ERS9293379", "ERP133910", "PRJEB49404", "Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model", "E-MTAB-7464_2", "Transcriptome Analysis", "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.", "ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03", null, "Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 \u00b5M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure \u201cAppendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent\u201d in RNeasy\u00ae Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "7dpa 1", "SAMEA11646672", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646672|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 1|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model", "E MTAB 7464 2:7dpa 1 p", "7dpa 1 p", "Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model", "Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "ERP133910", "NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model", "ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03", "7dpa-1_1.fastq.gz 7dpa-1_2.fastq.gz", "fastq fastq", 11533139040.0, 72082119.0, "E MTAB 7464 2:7dpa 1 ", "0:80 1:80", "A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102", 80, 80, null, null, 3069170319, 2575356466, 2889466424, 2996503729, 2642102, "ERX7289613", "ERS9293379", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.86542, 0.86857, 0.33902, 0.34263, 0.7288, 0.74186, 0.50529, 0.50071, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2022-12-29", "Adult", "Adult", "Multi-tissue", "Multi-system"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["10358"], "units": {}, "query_ms": 9.745857998495921}