{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\" and tissue_curation_coarse = \"Multi-system\"", "rows": [[9343, "ERR2935792", "ERX2938586", "ERS2922622", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Cnt mRNA ML 4", "SAMEA5138255", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138255|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:Cnt mRNA ML 4 p", "Cnt mRNA ML 4 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. 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Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. 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They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Cnt mRNA ML 3", "SAMEA5138254", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138254|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:Cnt mRNA ML 3 p", "Cnt mRNA ML 3 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. 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Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. 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They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Cnt mRNA ML 2", "SAMEA5138253", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138253|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:Cnt mRNA ML 2 p", "Cnt mRNA ML 2 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. 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They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Cnt mRNA ML 1", "SAMEA5138252", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138252|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:Cnt mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:Cnt mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:Cnt mRNA ML 1 p", "Cnt mRNA ML 1 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. 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RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "7dpa mRNA ML 4", "SAMEA5138251", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138251|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:7dpa mRNA ML 4 p", "7dpa mRNA ML 4 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "7dpa-mRNA-ML-4_1.fastq.gz 7dpa-mRNA-ML-4_2.fastq.gz", "fastq fastq", 11636085120.0, 72725532.0, "E MTAB 7464:7dpa mRNA ML 4 ", "0:80 1:80", "A:3154141550;C:2591688923;G:2792349992;T:3095216690;N:2687965", 80, 80, null, null, 3154141550, 2591688923, 2792349992, 3095216690, 2687965, "ERX2938582", "ERS2922618", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.8808, 0.88291, 0.28917, 0.2893, 0.73377, 0.74097, 0.50493, 0.4989, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9348, "ERR2935787", "ERX2938581", "ERS2922617", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "7dpa mRNA ML 3", "SAMEA5138250", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138250|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:7dpa mRNA ML 3 p", "7dpa mRNA ML 3 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "7dpa-mRNA-ML-3_1.fastq.gz 7dpa-mRNA-ML-3_2.fastq.gz", "fastq fastq", 9873881440.0, 61711759.0, "E MTAB 7464:7dpa mRNA ML 3 ", "0:80 1:80", "A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103", 80, 80, null, null, 2682240945, 2177286149, 2380282226, 2631847017, 2225103, "ERX2938581", "ERS2922617", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.83715, 0.84278, 0.34243, 0.34676, 0.73764, 0.75041, 0.50878, 0.49819, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9349, "ERR2935786", "ERX2938580", "ERS2922616", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "7dpa mRNA ML 2", "SAMEA5138249", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138249|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:7dpa mRNA ML 2 p", "7dpa mRNA ML 2 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "7dpa-mRNA-ML-2_2.fastq.gz 7dpa-mRNA-ML-2_1.fastq.gz", "fastq fastq", 12193073280.0, 76206708.0, "E MTAB 7464:7dpa mRNA ML 2 ", "0:80 1:80", "A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188", 80, 80, null, null, 3333326821, 2692186511, 2887657057, 3277111703, 2791188, "ERX2938580", "ERS2922616", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.8495, 0.851, 0.36393, 0.36549, 0.72466, 0.73582, 0.50377, 0.4964, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9350, "ERR2935785", "ERX2938579", "ERS2922615", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "7dpa mRNA ML 1", "SAMEA5138248", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138248|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:7dpa mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:7dpa mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:7dpa mRNA ML 1 p", "7dpa mRNA ML 1 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:7|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "7dpa-mRNA-ML-1_1.fastq.gz 7dpa-mRNA-ML-1_2.fastq.gz", "fastq fastq", 11533139040.0, 72082119.0, "E MTAB 7464:7dpa mRNA ML 1 ", "0:80 1:80", "A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102", 80, 80, null, null, 3069170319, 2575356466, 2889466424, 2996503729, 2642102, "ERX2938579", "ERS2922615", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.86529, 0.86845, 0.33913, 0.34252, 0.72928, 0.74194, 0.50425, 0.50214, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9351, "ERR2935784", "ERX2938578", "ERS2922614", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "1dpa mRNA ML 4", "SAMEA5138247", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138247|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 4|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:1dpa mRNA ML 4 p", "1dpa mRNA ML 4 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "1dpa-mRNA-ML-4_1.fastq.gz 1dpa-mRNA-ML-4_2.fastq.gz", "fastq fastq", 13728291840.0, 85801824.0, "E MTAB 7464:1dpa mRNA ML 4 ", "0:80 1:80", "A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856", 80, 80, null, null, 3747242594, 3041779368, 3248651209, 3687437813, 3180856, "ERX2938578", "ERS2922614", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90774, 0.91111, 0.34968, 0.34939, 0.72809, 0.73472, 0.50073, 0.49547, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9352, "ERR2935783", "ERX2938577", "ERS2922613", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "1dpa mRNA ML 3", "SAMEA5138246", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138246|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 3|scientific name:Danio rerio|sex:male|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:1dpa mRNA ML 3 p", "1dpa mRNA ML 3 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "1dpa-mRNA-ML-3_2.fastq.gz 1dpa-mRNA-ML-3_1.fastq.gz", "fastq fastq", 12524780320.0, 78279877.0, "E MTAB 7464:1dpa mRNA ML 3 ", "0:80 1:80", "A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636", 80, 80, null, null, 3452368285, 2754592593, 2905324477, 3409605329, 2889636, "ERX2938577", "ERS2922613", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90778, 0.91013, 0.32736, 0.3259, 0.73724, 0.74251, 0.51117, 0.51031, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9353, "ERR2935782", "ERX2938576", "ERS2922612", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "1dpa mRNA ML 2", "SAMEA5138245", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138245|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 2|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:1dpa mRNA ML 2 p", "1dpa mRNA ML 2 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "1dpa-mRNA-ML-2_1.fastq.gz 1dpa-mRNA-ML-2_2.fastq.gz", "fastq fastq", 15395445120.0, 96221532.0, "E MTAB 7464:1dpa mRNA ML 2 ", "0:80 1:80", "A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844", 80, 80, null, null, 4187891415, 3447519966, 3632085998, 4124408897, 3538844, "ERX2938576", "ERS2922612", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90197, 0.90707, 0.33526, 0.33624, 0.7371, 0.74479, 0.51163, 0.50652, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9354, "ERR2935781", "ERX2938575", "ERS2922611", "ERP112367", "PRJEB30004", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E-MTAB-7464", "Transcriptome Analysis", "Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. Here we aim to perform a detailed investigation of the transcriptome data obtained from early and late stages of zebrafish brain and melanocyte regeneration samples.", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", null, "Protocols: For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "1dpa mRNA ML 1", "SAMEA5138244", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2020 11 28T04:04:08Z|ENA LAST UPDATE:2018 11 28T11:38:53Z|External Id:SAMEA5138244|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2020 11 28T04:04:08Z|INSDC last update:2018 11 28T11:38:53Z|INSDC status:public|Submitter Id:E MTAB 7464:1dpa mRNA ML 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:Chemical ablation|organism part:caudal fin|sample name:E MTAB 7464:1dpa mRNA ML 1|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "E MTAB 7464:1dpa mRNA ML 1 p", "1dpa mRNA ML 1 p", "RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "For stab wound approach firstly fish were anesthetized by using Tricaine Sigma. A 30 gauge syringe needle was pushed through a nostril along the rostrocaudal body axis until the end of the one hemisphere of telencephalon. Then they were allowed for recovery of the wound in fresh water. At 3dpl and 14dpl day post lesion their stab lesioned hemispheres were dissected as early and late stage respectively. They were put into RNAlater solution immediately to prevent tissue degradation. For melanocyte regeneration Zebrafish melanocytes were chemically ablated by one day NCP treatment. NCP was washed post 24 hours of treatment. NCP Sigma Aldrich was prepared as 100 mM stock solutions in DMSO. Final concentration of NCP was used as 100 \u00b5M for each group. The early and late stages of melanocyte regeneration were determined as 1 day post ablation dpa and 7 days post ablation respectively. Firstly fish were anesthetized by Tricaine. Once fish were immobilized the caudal fin of each fish were resected and fins were placed into QIAzol Lysis Reagent and immediately proceeded to tissue disruption and homogenization. post homogenization of all brain and melanocyte tissues their RNAs were isolated by RNeasy\u00ae Micro Kit QIAGEN. The RNA quality and integrity were checked by the Agilent 2100 Bioanalyzer System. Adult zebrafish were fed under normal conditions 1 micromolar Neocuproine for some samples RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina", "Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: injury:chemical ablation|Experimental Factor: time:1|Experimental Factor: organism part:caudal fin", "ssRNA-seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", "1600FApplication ReadForward11RApplication ReadReverse81", "ERP112367", "NextSeq 500 paired end sequencing; RNA seq to investigate the genetic pathways in brain and melanocyte regeneration using a zebrafish model", "ENA FIRST PUBLIC:2023 08 24|ENA LAST UPDATE:2023 08 24", "1dpa-mRNA-ML-1_2.fastq.gz 1dpa-mRNA-ML-1_1.fastq.gz", "fastq fastq", 9835056000.0, 61469100.0, "E MTAB 7464:1dpa mRNA ML 1 ", "0:80 1:80", "A:2673004774;C:2192168640;G:2335585327;T:2632030261;N:2266998", 80, 80, null, null, 2673004774, 2192168640, 2335585327, 2632030261, 2266998, "ERX2938575", "ERS2922611", "ERA1667271", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.89673, 0.89924, 0.33937, 0.33954, 0.72342, 0.73032, 0.49857, 0.48103, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Turkey", "2018-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [10206, "ERR6474244", "ERX6101519", "ERS7377049", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "InputFISH", "E MTAB 10834:InputFISH", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:InputFISH p", "InputFISH p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:input DNA|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "InputFISH.R1.fastq.gz InputFISH.R2.fastq.gz", "fastq fastq", 2014534500.0, 24271500.0, "E MTAB 10834:InputFISH.R", "0:40 1:43", "A:435725523;C:539145149;G:601092466;T:438298953;N:272409", 40, 43, null, null, 435725523, 539145149, 601092466, 438298953, 272409, "ERX6101519", "ERS7377049", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.394, 0.34957, 0.09053, 0.09378, 0.96485, 0.97323, 0.73467, 0.62676, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10207, "ERR6474223", "ERX6101498", "ERS7377028", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "hsHuRFISH rep2", "E MTAB 10834:hsHuRFISH rep2", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:hsHuRFISH rep2 p", "hsHuRFISH rep2 p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "hsHuRFISH_rep2.R2.fastq.gz hsHuRFISH_rep2.R1.fastq.gz", "fastq fastq", 2106598100.0, 25380700.0, "E MTAB 10834:hsHuRFISH rep2.R", "0:40 1:43", "A:503141361;C:548220448;G:569927989;T:485014455;N:293847", 40, 43, null, null, 503141361, 548220448, 569927989, 485014455, 293847, "ERX6101498", "ERS7377028", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.76055, 0.70626, 0.18785, 0.18742, 0.92387, 0.93533, 0.72831, 0.65481, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10208, "ERR6474222", "ERX6101497", "ERS7377027", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "hsHuRFISH rep1", "E MTAB 10834:hsHuRFISH rep1", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:hsHuRFISH rep1 p", "hsHuRFISH rep1 p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "hsHuRFISH_rep1.R1.fastq.gz hsHuRFISH_rep1.R2.fastq.gz", "fastq fastq", 2520623431.0, 30368957.0, "E MTAB 10834:hsHuRFISH rep1.R", "0:40 1:43", "A:604086659;C:653262791;G:679919989;T:582992802;N:361190", 40, 43, null, null, 604086659, 653262791, 679919989, 582992802, 361190, "ERX6101497", "ERS7377027", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.76096, 0.70783, 0.18844, 0.18848, 0.92101, 0.93275, 0.7333, 0.62616, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10209, "ERR6474221", "ERX6101496", "ERS7377026", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "HaloFISH", "E MTAB 10834:HaloFISH", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:HaloFISH p", "HaloFISH p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:anti HaloTag|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "HaloFISH.R2.fastq.gz HaloFISH.R1.fastq.gz", "fastq fastq", 2353027590.0, 28349730.0, "E MTAB 10834:HaloFISH.R", "0:40 1:43", "A:522964401;C:650152942;G:677020220;T:502555313;N:334714", 40, 43, null, null, 522964401, 650152942, 677020220, 502555313, 334714, "ERX6101496", "ERS7377026", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.82307, 0.78117, 0.18309, 0.18609, 0.93888, 0.94627, 0.73861, 0.63812, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10210, "ERR6474216", "ERX6101492", "ERS7377022", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "drHuRFISH rep2", "E MTAB 10834:drHuRFISH rep2", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:drHuRFISH rep2 p", "drHuRFISH rep2 p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "drHuRFISH_rep2.R1.fastq.gz drHuRFISH_rep2.R2.fastq.gz", "fastq fastq", 2408024386.0, 29012342.0, "E MTAB 10834:drHuRFISH rep2.R", "0:40 1:43", "A:566287649;C:627743498;G:663052609;T:550604982;N:335648", 40, 43, null, null, 566287649, 627743498, 663052609, 550604982, 335648, "ERX6101492", "ERS7377022", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.68524, 0.62721, 0.16916, 0.1656, 0.93501, 0.94541, 0.7028, 0.64738, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10211, "ERR6474215", "ERX6101491", "ERS7377021", "ERP131171", "PRJEB46937", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E-MTAB-10834", "Other", "RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform. In this study RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1 IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets. In addition a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1 hence with RAP seq we also report T7 RAP seq.", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, "Protocols: HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "drHuRFISH rep1", "E MTAB 10834:drHuRFISH rep1", null, "isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "E MTAB 10834:drHuRFISH rep1 p", "drHuRFISH rep1 p", "RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "HepG2 were obtained from American Type Culture Collection ATCC Rockville MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 \u00b0C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S Sigma and 10 % fetal bovine serum Hyclone GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week done by aspirating the medium gently washing the cells with phosphate buffered saline PBS without xxx+ Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05% Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM Magnesium Chloride 10 mM pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions then AMPure cleaned and aliquoted and stored at 80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS 0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation the beads are washed 4 times twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest 700 \u00b5L Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 \u00b0C or RNA extraction was continued immediately by adding 140 \u00b5L chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min before centrifugation at 9.000 g for 5 min at 4 \u00b0C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 \u00b0C for 10 min and the supernatant discarded. The pellet was washed in 700 \u00b5L cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 \u00b0C. The supernatant was discarded entirely and the pellet air dried for 5 minutes before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 \u00b0C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3 PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.", "Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP131171", "NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA", "ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11", "drHuRFISH_rep1.R1.fastq.gz drHuRFISH_rep1.R2.fastq.gz", "fastq fastq", 3025188980.0, 36448060.0, "E MTAB 10834:drHuRFISH rep1.R", "0:40 1:43", "A:720153781;C:784188971;G:824077525;T:696330222;N:438481", 40, 43, null, null, 720153781, 784188971, 824077525, 696330222, 438481, "ERX6101491", "ERS7377021", "ERA5607540", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", "Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive", 2, 0.7001, 0.64217, 0.17626, 0.1728, 0.93154, 0.94249, 0.72494, 0.65821, 40, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Sweden", "2023-08-11", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [10342, "ERR7720665", "ERX7289629", "ERS9293395", "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", "Nevi 3", "SAMEA11646688", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646688|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:Nevi 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 3|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:Nevi 3 p", "Nevi 3 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus", "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", "Nevi-3_1.fastq.gz Nevi-3_2.fastq.gz", "fastq fastq", 8483600160.0, 53022501.0, "E MTAB 7464 2:Nevi 3 ", "0:80 1:80", "A:2299114269;C:1922614492;G:1990271122;T:2270860686;N:739591", 80, 80, null, null, 2299114269, 1922614492, 1990271122, 2270860686, 739591, "ERX7289629", "ERS9293395", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93346, 0.93983, 0.10878, 0.10282, 0.72608, 0.72368, 0.45081, 0.44901, 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"], [10343, "ERR7720664", "ERX7289628", "ERS9293394", "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", "Nevi 2", "SAMEA11646687", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646687|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:Nevi 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 2|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:Nevi 2 p", "Nevi 2 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus", "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", "Nevi-2_1.fastq.gz Nevi-2_2.fastq.gz", "fastq fastq", 9002687680.0, 56266798.0, "E MTAB 7464 2:Nevi 2 ", "0:80 1:80", "A:2446965759;C:2045918133;G:2107744175;T:2400665463;N:1394150", 80, 80, null, null, 2446965759, 2045918133, 2107744175, 2400665463, 1394150, "ERX7289628", "ERS9293394", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93879, 0.94198, 0.1057, 0.10023, 0.7289, 0.72874, 0.45656, 0.45677, 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"], [10344, "ERR7720663", "ERX7289627", "ERS9293393", "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", "Nevi 1", "SAMEA11646686", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646686|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:Nevi 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 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:Nevi 1 p", "Nevi 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus", "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", "Nevi-1_1.fastq.gz Nevi-1_2.fastq.gz", "fastq fastq", 9332077600.0, 58325485.0, "E MTAB 7464 2:Nevi 1 ", "0:80 1:80", "A:2559136296;C:2096458598;G:2152359634;T:2522670596;N:1452476", 80, 80, null, null, 2559136296, 2096458598, 2152359634, 2522670596, 1452476, "ERX7289627", "ERS9293393", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93341, 0.93788, 0.12721, 0.12045, 0.71181, 0.71104, 0.45834, 0.46252, 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"], [10345, "ERR7720662", "ERX7289626", "ERS9293392", "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", "Melanoma 4", "SAMEA11646685", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646685|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:Melanoma 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 4|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:Melanoma 4 p", "Melanoma 4 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma", "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", "Melanoma-4_1.fastq.gz Melanoma-4_2.fastq.gz", "fastq fastq", 8435873280.0, 52724208.0, "E MTAB 7464 2:Melanoma 4 ", "0:80 1:80", "A:2339229980;C:1858003608;G:1925352938;T:2311974102;N:1312652", 80, 80, null, null, 2339229980, 1858003608, 1925352938, 2311974102, 1312652, "ERX7289626", "ERS9293392", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93101, 0.93509, 0.11646, 0.10875, 0.73647, 0.73742, 0.5229, 0.52491, 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"], [10346, "ERR7720661", "ERX7289625", "ERS9293391", "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", "Melanoma 3", "SAMEA11646684", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646684|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:Melanoma 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 3|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:Melanoma 3 p", "Melanoma 3 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma", "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", "Melanoma-3_1.fastq.gz Melanoma-3_2.fastq.gz", "fastq fastq", 8652678880.0, 54079243.0, "E MTAB 7464 2:Melanoma 3 ", "0:80 1:80", "A:2358154757;C:1941914032;G:2017842865;T:2333420807;N:1346419", 80, 80, null, null, 2358154757, 1941914032, 2017842865, 2333420807, 1346419, "ERX7289625", "ERS9293391", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93095, 0.93482, 0.11494, 0.10979, 0.74878, 0.74801, 0.54149, 0.54333, 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"], [10347, "ERR7720660", "ERX7289624", "ERS9293390", "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", "Melanoma 2", "SAMEA11646683", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646683|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:Melanoma 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 2|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:Melanoma 2 p", "Melanoma 2 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma", "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", "Melanoma-2_1.fastq.gz Melanoma-2_2.fastq.gz", "fastq fastq", 9474565280.0, 59216033.0, "E MTAB 7464 2:Melanoma 2 ", "0:80 1:80", "A:2592490883;C:2143181332;G:2197827206;T:2539575741;N:1490118", 80, 80, null, null, 2592490883, 2143181332, 2197827206, 2539575741, 1490118, "ERX7289624", "ERS9293390", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93925, 0.94448, 0.10906, 0.10386, 0.73768, 0.73722, 0.51879, 0.51954, 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"], [10348, "ERR7720659", "ERX7289623", "ERS9293389", "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", "Melanoma 1", "SAMEA11646682", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646682|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:Melanoma 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 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:Melanoma 1 p", "Melanoma 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:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma", "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", "Melanoma-1_1.fastq.gz Melanoma-1_2.fastq.gz", "fastq fastq", 8202724480.0, 51267028.0, "E MTAB 7464 2:Melanoma 1 ", "0:80 1:80", "A:2226523748;C:1862763739;G:1929197629;T:2182962113;N:1277251", 80, 80, null, null, 2226523748, 1862763739, 1929197629, 2182962113, 1277251, "ERX7289623", "ERS9293389", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93514, 0.9398, 0.10447, 0.09961, 0.71697, 0.71715, 0.50157, 0.50305, 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"], [10349, "ERR7720658", "ERX7289622", "ERS9293388", "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", "Ctrl R 4", "SAMEA11646681", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646681|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:Ctrl R 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 4|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:Ctrl R 4 p", "Ctrl R 4 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:n1|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", "Ctrl-R-4_1.fastq.gz Ctrl-R-4_2.fastq.gz", "fastq fastq", 12134105440.0, 75838159.0, "E MTAB 7464 2:Ctrl R 4 ", "0:80 1:80", "A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860", 80, 80, null, null, 3262023701, 2677095735, 2964643096, 3227367048, 2975860, "ERX7289622", "ERS9293388", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.91148, 0.90942, 0.31684, 0.30692, 0.7517, 0.75708, 0.51896, 0.51898, 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"], [10350, "ERR7720657", "ERX7289621", "ERS9293387", "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", "Ctrl R 3", "SAMEA11646680", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646680|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:Ctrl R 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 3|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:Ctrl R 3 p", "Ctrl R 3 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:n1|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", "Ctrl-R-3_1.fastq.gz Ctrl-R-3_2.fastq.gz", "fastq fastq", 10198941920.0, 63743387.0, "E MTAB 7464 2:Ctrl R 3 ", "0:80 1:80", "A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227", 80, 80, null, null, 2707258482, 2295053882, 2521099885, 2673029444, 2500227, "ERX7289621", "ERS9293387", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.88031, 0.87949, 0.30603, 0.30519, 0.76219, 0.76798, 0.52516, 0.51963, 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"], [10351, "ERR7720656", "ERX7289620", "ERS9293386", "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", "Ctrl R 2", "SAMEA11646679", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646679|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:Ctrl R 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 2|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:Ctrl R 2 p", "Ctrl R 2 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:n1|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", "Ctrl-R-2_1.fastq.gz Ctrl-R-2_2.fastq.gz", "fastq fastq", 13001272960.0, 81257956.0, "E MTAB 7464 2:Ctrl R 2 ", "0:80 1:80", "A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729", 80, 80, null, null, 3429977204, 2902807573, 3288394622, 3376870832, 3222729, "ERX7289620", "ERS9293386", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.89444, 0.89377, 0.30516, 0.30529, 0.75773, 0.76769, 0.52784, 0.52192, 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"], [10352, "ERR7720655", "ERX7289619", "ERS9293385", "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", "Ctrl R 1", "SAMEA11646678", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646678|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:Ctrl R 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 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:Ctrl R 1 p", "Ctrl R 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:n1|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", "Ctrl-R-1_1.fastq.gz Ctrl-R-1_2.fastq.gz", "fastq fastq", 10689399040.0, 66808744.0, "E MTAB 7464 2:Ctrl R 1 ", "0:80 1:80", "A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382", 80, 80, null, null, 2897858681, 2320332197, 2613694217, 2854881563, 2632382, "ERX7289619", "ERS9293385", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.87124, 0.87083, 0.30804, 0.30796, 0.74596, 0.75668, 0.49784, 0.50675, 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"], [10353, "ERR7720654", "ERX7289618", "ERS9293384", "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", "Ctrl MN 3", "SAMEA11646677", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646677|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:Ctrl MN 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 3|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:Ctrl MN 3 p", "Ctrl MN 3 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:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|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", "Ctrl-MN-3_1.fastq.gz Ctrl-MN-3_2.fastq.gz", "fastq fastq", 7551734240.0, 47198339.0, "E MTAB 7464 2:Ctrl MN 3 ", "0:80 1:80", "A:2046757744;C:1713576176;G:1763123655;T:2027090307;N:1186358", 80, 80, null, null, 2046757744, 1713576176, 1763123655, 2027090307, 1186358, "ERX7289618", "ERS9293384", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93513, 0.93893, 0.11198, 0.10677, 0.7232, 0.72267, 0.44068, 0.4478, 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"], [10354, "ERR7720653", "ERX7289617", "ERS9293383", "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", "Ctrl MN 2", "SAMEA11646676", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646676|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:Ctrl MN 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 2|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:Ctrl MN 2 p", "Ctrl MN 2 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:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|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", "Ctrl-MN-2_1.fastq.gz Ctrl-MN-2_2.fastq.gz", "fastq fastq", 8217322560.0, 51358266.0, "E MTAB 7464 2:Ctrl MN 2 ", "0:80 1:80", "A:2206636607;C:1895861057;G:1945883692;T:2167661877;N:1279327", 80, 80, null, null, 2206636607, 1895861057, 1945883692, 2167661877, 1279327, "ERX7289617", "ERS9293383", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.94029, 0.94525, 0.10143, 0.09713, 0.72251, 0.72036, 0.44465, 0.44591, 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"], [10355, "ERR7720652", "ERX7289616", "ERS9293382", "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", "Ctrl MN 1", "SAMEA11646675", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646675|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:Ctrl MN 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 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:Ctrl MN 1 p", "Ctrl MN 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:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|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", "Ctrl-MN-1_1.fastq.gz Ctrl-MN-1_2.fastq.gz", "fastq fastq", 8135337280.0, 50845858.0, "E MTAB 7464 2:Ctrl MN 1 ", "0:80 1:80", "A:2202274973;C:1853973619;G:1910166269;T:2167658174;N:1264245", 80, 80, null, null, 2202274973, 1853973619, 1910166269, 2167658174, 1264245, "ERX7289616", "ERS9293382", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.93729, 0.94287, 0.10448, 0.09933, 0.72585, 0.72612, 0.45373, 0.45518, 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"], [10356, "ERR7720651", "ERX7289615", "ERS9293381", "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 3", "SAMEA11646674", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646674|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 3|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 3|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 3 p", "7dpa 3 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-3_1.fastq.gz 7dpa-3_2.fastq.gz", "fastq fastq", 9873881440.0, 61711759.0, "E MTAB 7464 2:7dpa 3 ", "0:80 1:80", "A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103", 80, 80, null, null, 2682240945, 2177286149, 2380282226, 2631847017, 2225103, "ERX7289615", "ERS9293381", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.83718, 0.84277, 0.3425, 0.34639, 0.73801, 0.75035, 0.51021, 0.49835, 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"], [10357, "ERR7720650", "ERX7289614", "ERS9293380", "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 2", "SAMEA11646673", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646673|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 2|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 2|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 2 p", "7dpa 2 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-2_1.fastq.gz 7dpa-2_2.fastq.gz", "fastq fastq", 12193073280.0, 76206708.0, "E MTAB 7464 2:7dpa 2 ", "0:80 1:80", "A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188", 80, 80, null, null, 3333326821, 2692186511, 2887657057, 3277111703, 2791188, "ERX7289614", "ERS9293380", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.84944, 0.85085, 0.36391, 0.36512, 0.72496, 0.73511, 0.50367, 0.49643, 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"], [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"], [10359, "ERR7720648", "ERX7289612", "ERS9293378", "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", "1dpa 3", "SAMEA11646671", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646671|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 2:1dpa 3|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 2:1dpa 3|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 2:1dpa 3 p", "1dpa 3 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", "1dpa-3_1.fastq.gz 1dpa-3_2.fastq.gz", "fastq fastq", 13728291840.0, 85801824.0, "E MTAB 7464 2:1dpa 3 ", "0:80 1:80", "A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856", 80, 80, null, null, 3747242594, 3041779368, 3248651209, 3687437813, 3180856, "ERX7289612", "ERS9293378", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90779, 0.9111, 0.34976, 0.34957, 0.72827, 0.73499, 0.50071, 0.49578, 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"], [10360, "ERR7720647", "ERX7289611", "ERS9293377", "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", "1dpa 2", "SAMEA11646670", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646670|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 2:1dpa 2|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 2:1dpa 2|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 2:1dpa 2 p", "1dpa 2 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", "1dpa-2_1.fastq.gz 1dpa-2_2.fastq.gz", "fastq fastq", 12524780320.0, 78279877.0, "E MTAB 7464 2:1dpa 2 ", "0:80 1:80", "A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636", 80, 80, null, null, 3452368285, 2754592593, 2905324477, 3409605329, 2889636, "ERX7289611", "ERS9293377", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90773, 0.91019, 0.32749, 0.32608, 0.73756, 0.74172, 0.51153, 0.50818, 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"], [10361, "ERR7720646", "ERX7289610", "ERS9293376", "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", "1dpa 1", "SAMEA11646669", "Izmir Biomedicine and Genome Center / Turkey", "ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646669|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 2:1dpa 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 2:1dpa 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 2:1dpa 1 p", "1dpa 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", "1dpa-1_1.fastq.gz 1dpa-1_2.fastq.gz", "fastq fastq", 15395445120.0, 96221532.0, "E MTAB 7464 2:1dpa 1 ", "0:80 1:80", "A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844", 80, 80, null, null, 4187891415, 3447519966, 3632085998, 4124408897, 3538844, "ERX7289610", "ERS9293376", "ERA7895107", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", "Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive", 2, 0.90197, 0.907, 0.33556, 0.33653, 0.73724, 0.74546, 0.51071, 0.50585, 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"], [32781, "SRR29411985", "SRX24925451", "SRS21630866", "SRP513930", "PRJNA1124008", "Cell state transitions are decoupled from cell division during early embryo development [II]", "GSE269848", "Other", "Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.", null, "pubmed:37546736", null, "24 38 hpf and 48 hpf tails", "GSM8328864", null, "source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing", "24 38 hpf and 48 hpf tails", "Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section \"Single cell RNA seq Data preprocessing\" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode tag sequence and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode and associated metadata for all cells Library strategy: inDrops v3 scRNA seq", "embryo tail", null, "Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "tissue:embryo tail", "GSM8328864", "GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER", "GSM8328864 r1", "GSM8328864", "1", "Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513930", null, null, "Undetermined_S0_L002_R1_001.fastq.gz Undetermined_S0_L002_R2_001.fastq.gz Undetermined_S0_L002_R3_001.fastq.gz Undetermined_S0_L002_R4_001.fastq.gz", "fastq fastq fastq fastq", 58603546956.0, 505202991.0, "GSM8328864 r1", "0:86 1:8 2:8 3:14", "A:13191204330;C:9162028793;G:9431065581;T:11662090182;N:1068340", 86, 8, 8, 14, 13191204330, 9162028793, 9431065581, 11662090182, 1068340, "SRX24925451", "SRS21630866", "SRA1899240", "Harvard University", "Harvard University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2024-06-14", "Multi-stage", "Embryo", "Tail", "Multi-system"], [32782, "SRR29411986", "SRX24925451", "SRS21630866", "SRP513930", "PRJNA1124008", "Cell state transitions are decoupled from cell division during early embryo development [II]", "GSE269848", "Other", "Paper abstract: As tissues develop cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. However in the absence of cell division differentiation slows down in some cell types and cells exhibit global stress responses. While differentiation is robust to blocking cell division the proportions of cells across cell states are not but show evidence of partial compensation. This work clarifies our understanding of the role of cell division in development and showcases the utility of combining embryo wide perturbations with single cell RNA sequencing to uncover the role of common biological processes across multiple tissues. Overall design: Design of experiment for this particular dataset: Forty tails from zebrafish embryos at 24 38 hpf and 48 hpf were collected. Cells were dissociated from these tails and multi seq tags were added to the cells for each time point. Cells from all time points were pooled and single cell sequencing was performed using Indrops. Four gene expression GEX libraries were prepared for transcriptomic information and four multiseq tag libraries TAG were prepared for reading out the multiseq tags. We provide the raw data .fastq files processed data both raw counts.tsv.gz and filtered by total UMI counts filtered.h5ad files and the entire filtered data post removing doublets as all data.h5ad. We also provide counts for multi seq tags example TAG 1.counts.csv. Information about pooling libraries and library indices is provided in Pooling Samples.xlsx. Only 24 hpf data was used for Kukreja et. al. 2024 and hence the cell state information we provide in the all data.h5ad is only for 24 hpf.", null, "pubmed:37546736", null, "24 38 hpf and 48 hpf tails", "GSM8328864", null, "source name:embryo tail|tissue:embryo tail|geo loc name:missing|collection date:missing", "24 38 hpf and 48 hpf tails", "Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files 2 lanes x 4 reads per lane. The read files from an inDrops run have the following content: * R1 001.fastq.gz : contains the three prime UTR cDNA read * R2 001.fastq.gz : contains the first half of the cell barcode * R3 001.fastq.gz : contains the library index for demultiplexing libraries * R4 001.fastq.gz : contains the second half of the barcode and the UMI. All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis github.com/indrops. Single cell transcriptomes were barcoded using inDrops Klein et al Cell 2015. Standard transcriptome RNA seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1 14 cycles for Read2 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline github.com/indrops/indrops. Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly Assembly Accession: GCF 000002035.5 using bowtie version 1.1.143. To obtain the final counts matrix used for data analysis total count filters were applied as described in Kukreja et. al. 2024 method section \"Single cell RNA seq Data preprocessing\" Assembly: GRCz10 genome assembly Assembly Accession: GCF 000002035.5 Supplementary files format and content: Raw counts for transcriptome tsv.gz: cell barcode gene names and raw counts for all cells Supplementary files format and content: Raw counts for multi seq tags csv.gz: cell barcode tag sequence and raw counts for all cells Supplementary files format and content: Filtered barcodes filtered.h5ad: cell barcode and associated metadata for all cells Library strategy: inDrops v3 scRNA seq", "embryo tail", null, "Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "tissue:embryo tail", "GSM8328864", "GSM8328864: 24 38 hpf and 48 hpf tails; Danio rerio; OTHER", "GSM8328864 r1", "GSM8328864", "1", "Forty zebrafish tail samples collected at 24 38 hpf and 48 hpf were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. 2018. Briefly the tails were dissociated with a mixture of DNaseI 20\u00b5g/mL Collagenase/Dispase 8 mg/mL and 0.25% Trypsin EDTA at 30.5\u00b0C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi seq. The barcoded samples were subsequently pooled washed with 1% BSA + PBS and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of 300 000 cells/mL. Single cell transcriptomes were captured using inDrops. NGS libraries were prepared by the Single cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP513930", null, null, "Undetermined_S0_L001_R1_001.fastq.gz Undetermined_S0_L001_R2_001.fastq.gz Undetermined_S0_L001_R3_001.fastq.gz Undetermined_S0_L001_R4_001.fastq.gz", "fastq fastq fastq fastq", 44072422880.0, 379934680.0, "GSM8328864 r2", "0:86 1:8 2:8 3:14", "A:9919784228;C:6894965731;G:7094749745;T:8764100624;N:782152", 86, 8, 8, 14, 9919784228, 6894965731, 7094749745, 8764100624, 782152, "SRX24925451", "SRS21630866", "SRA1899240", "Harvard University", "Harvard University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "trueseq", "sc", "single_cell_droplet", "indrops", null, "United States", "2024-06-14", "Multi-stage", "Embryo", "Tail", "Multi-system"], [43987, "SRR6811828", "SRX3768868", "SRS3023414", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Pancreas 3 exo scar", "GSM3032171", null, "source name:Pancreas except primary islet liver|strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult", "Pancreas 3 exo scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Pancreas except primary islet liver", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult", "GSM3032171", "GSM3032171: Pancreas 3 exo scar; Danio rerio; OTHER", "GSM3032171", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032171", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "P7exo_scar_R1.fastq.gz P7exo_scar_R2.fastq.gz", "fastq fastq", 4291410352.0, 34608148.0, "GSM3032171 r1", "0:26 1:98", "A:1266869162;C:1345773385;G:950601988;T:726078376;N:2087441", 26, 98, null, null, 1266869162, 1345773385, 950601988, 726078376, 2087441, "SRX3768868", "SRS3023414", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 0.00014, 0.00241, 0.00012, 0.00024, 0.99995, 0.99691, 0.0, 0.65306, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-03-06", "Adult", "Adult", "Multi-tissue", "Multi-system"], [43989, "SRR6811826", "SRX3768866", "SRS3023382", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Heart 3 scar", "GSM3032169", null, "source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "Heart 3 scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Heart and blood", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM3032169", "GSM3032169: Heart 3 scar; Danio rerio; OTHER", "GSM3032169", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032169", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "H7_scar_R1.fastq.gz H7_scar_R2.fastq.gz", "fastq fastq", 3999397296.0, 32253204.0, "GSM3032169 r1", "0:26 1:98", "A:1170970784;C:1255843391;G:881154893;T:689473188;N:1955040", 26, 98, null, null, 1170970784, 1255843391, 881154893, 689473188, 1955040, "SRX3768866", "SRS3023382", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 0.00018, 0.00228, 0.00015, 0.00019, 0.99991, 0.99659, 0.8, 0.67235, 26, 98, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-03-06", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44008, "SRR6211484", "SRX3320759", "SRS2626332", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Heart 2 scar", "GSM2830055", null, "source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "Heart 2 scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. In the fourth filtering step we determined the distribution of reads for the scars we had kept so far. Based on this distribution we set a cut off and filtered out the scars that did not have at least this number of reads. Finally for each cell type we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Heart and blood", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM2830055", "GSM2830055: Heart 2 scar; Danio rerio; OTHER", "GSM2830055", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830055", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "H6_scar_R1.fastq.gz H6_scar_R2.fastq.gz", "fastq fastq", 2079107172.0, 15065994.0, "GSM2830055 r1", "0:28 1:110", "A:580640871;C:641740953;G:501505035;T:355092832;N:127481", 28, 110, null, null, 580640871, 641740953, 501505035, 355092832, 127481, "SRX3320759", "SRS2626332", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 5e-05, 0.00253, 4e-05, 0.00023, 1.0, 0.99778, null, 0.58419, 28, 110, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44009, "SRR6211483", "SRX3320758", "SRS2626348", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Pancreas 2 scar", "GSM2830054", null, "source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "Pancreas 2 scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. In the fourth filtering step we determined the distribution of reads for the scars we had kept so far. Based on this distribution we set a cut off and filtered out the scars that did not have at least this number of reads. Finally for each cell type we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Pancreas and liver", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "GSM2830054", "GSM2830054: Pancreas 2 scar; Danio rerio; OTHER", "GSM2830054", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830054", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "P6_scar_R1.fastq.gz P6_scar_R2.fastq.gz", "fastq fastq", 1026715860.0, 7439970.0, "GSM2830054 r1", "0:28 1:110", "A:287816843;C:320879355;G:243598630;T:174359452;N:61580", 28, 110, null, null, 287816843, 320879355, 243598630, 174359452, 61580, "SRX3320758", "SRS2626348", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 0.00029, 0.00123, 0.00028, 6e-05, 1.0, 0.99914, null, 0.25714, 28, 110, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44010, "SRR6211482", "SRX3320757", "SRS2626331", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Heart 1 scar", "GSM2830053", null, "source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "Heart 1 scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. In the fourth filtering step we determined the distribution of reads for the scars we had kept so far. Based on this distribution we set a cut off and filtered out the scars that did not have at least this number of reads. Finally for each cell type we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Heart and blood", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM2830053", "GSM2830053: Heart 1 scar; Danio rerio; OTHER", "GSM2830053", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830053", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "H5_scar_R1.fastq.gz H5_scar_R2.fastq.gz", "fastq fastq", 1287546624.0, 10218624.0, "GSM2830053 r1", "0:26 1:100", "A:365272675;C:413037677;G:296495693;T:212570153;N:170426", 26, 100, null, null, 365272675, 413037677, 296495693, 212570153, 170426, "SRX3320757", "SRS2626331", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 0.00023, 0.00044, 0.00022, 3e-05, 1.0, 0.99955, null, 0.32653, 26, 100, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [44012, "SRR6211480", "SRX3320755", "SRS2626329", "SRP121343", "PRJNA415636", "Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars", "GSE106121", "Other", "A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.", null, "pubmed:29644996", null, "Pancreas 1 scar", "GSM2830051", null, "source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "Pancreas 1 scar", "Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped had an incorrect barcode or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step we aimed to remove easily recognizable sequencing errors. To this end we consecutively considered scar sequences that have the same cellular barcode and UMI UMIs that have the same cellular barcode and scar sequence and cellular barcodes that have the same UMI and scar sequence. In each step we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus but information about scar expression levels was not required in our downstream analysis. In the third filtering step we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript? Do both scars occur in cells independently from each other? Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true the scars were kept and the sequences were placed on a list of validated scars that if they occurred in the same cell in another library did not have to be tested anymore. If one or zero criteria were true the scar that had only one transcript or the scar that did not occur independently were filtered out. In the fourth filtering step we determined the distribution of reads for the scars we had kept so far. Based on this distribution we set a cut off and filtered out the scars that did not have at least this number of reads. Finally for each cell type we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode scar name cell type scar probability and number of organisms that have this cell.", "Pancreas and liver", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "GSM2830051", "GSM2830051: Pancreas 1 scar; Danio rerio; OTHER", "GSM2830051", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830051", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "P5_scar_R1.fastq.gz P5_scar_R2.fastq.gz", "fastq fastq", 1192602600.0, 9465100.0, "GSM2830051 r1", "0:26 1:100", "A:346841760;C:383266222;G:268916933;T:193424756;N:152929", 26, 100, null, null, 346841760, 383266222, 268916933, 193424756, 152929, "SRX3320755", "SRS2626329", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 2, 0.00021, 0.00091, 0.00014, 2e-05, 0.99997, 0.99892, 0.0, 0.23931, 26, 100, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2017-10-24", "Adult", "Adult", "Multi-tissue", "Multi-system"], [50874, "SRR8356798", "SRX5167561", "SRS4175446", "SRP173971", "PRJNA510841", "Transcription factor induction of vascular blood stem cell niches in vivo [TOMO Seq]", "GSE124150", "Other", "We report RNA tomography tomo seq gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue CHT was isolated by manual dissection snap froze and then cryosections 40 in total 8 \u00b5m thick were collected along the dorsal ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing. Overall design: The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method Junker et al. 2014.", "parent bioproject:PRJNA510836", null, null, "Tomo seq zebrafish tail at 72 hpf", "GSM3521717", null, "source name:mpx:GFP transgenic zebrafish embryo wild type Casper background|tissue:tail|developmental stage:72 hpf", "Tomo seq zebrafish tail at 72 hpf", "Library strategy: RNA tomography tomo seq Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in the Junker et al. 2014. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 Mapping and demultiplexing were done as described in Gr\u00fcn et al. Validation of noise models for single cell transcriptomics Nature Methods 2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0 where script tomo.sh is an example for how to run the mapping scripts. Genome build: zv9", "mpx:GFP transgenic zebrafish embryo wild type Casper background", "No treatment", "The total RNA from individual cryosections 40 in total each 8 \u00b5m thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.", "mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap frozen on dry ice.", "tissue:tail|developmental stage:72 hpf", "GSM3521717", "GSM3521717: Tomo seq zebrafish tail at 72 hpf; Danio rerio; OTHER", "GSM3521717", null, "1", "The total RNA from individual cryosections 40 in total each 8 \u00b5m thick was extracted using Trizol reagent. The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described Junker et al. 2014.", "GEO Accession:GSM3521717", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP173971", null, null, null, null, 3762222874.0, 24959737.0, "GSM3521717 r1", "0:75.36 1:75.37", "A:1160852277;C:485683733;G:556965887;T:1558649449;N:71528", 75, 75, null, null, 1160852277, 485683733, 556965887, 1558649449, 71528, "SRX5167561", "SRS4175446", "SRA825234", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.20644, 0.76788, 0.14917, 0.11551, 0.98169, 0.8382, 0.50072, 0.52728, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc", "single_cell_plate", "celseq", null, "United States", "2018-12-19", "Larval", "Larval", "Tail", "Multi-system"], [59501, "SRR11924323", "SRX8469995", "SRS6770646", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Adult tail 2", "GSM4591062", null, "source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "Adult tail 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "adult tail trunk", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591062", "GSM4591062: Adult tail 2; Danio rerio; OTHER", "GSM4591062", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591062", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "Adult_tail_2.bam GSE151797_Reference_sequence.fa", "bam bam", 156647953.0, 5517527.0, "GSM4591062 r1", "0:28.39", "A:32903673;C:49609293;G:39096775;T:35038212;N:0", 28, null, null, null, 32903673, 49609293, 39096775, 35038212, 0, "SRX8469995", "SRS6770646", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.80662, null, 0.20653, null, 0.88722, null, 0.58074, null, 37, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Adult", "Adult", "Multi-tissue", "Multi-system"], [59502, "SRR11924321", "SRX8469994", "SRS6770645", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Adult tail 1", "GSM4591061", null, "source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "Adult tail 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "adult tail trunk", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591061", "GSM4591061: Adult tail 1; Danio rerio; OTHER", "GSM4591061", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591061", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "Adult_tail_1.bam GSE151797_Reference_sequence.fa", "bam bam", 50029636.0, 1968329.0, "GSM4591061 r1", "0:25.42", "A:9571393;C:14825016;G:13276309;T:12356918;N:0", 25, null, null, null, 9571393, 14825016, 13276309, 12356918, 0, "SRX8469994", "SRS6770645", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.46312, null, 0.12127, null, 0.91806, null, 0.67424, null, 44, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Adult", "Adult", "Multi-tissue", "Multi-system"]], "truncated": false, "filtered_table_rows_count": 49, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_selection\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "other", "p1": "Multi-system"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "ssRNA-seq", "label": "ssRNA-seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system&experiment.library_strategy=ssRNA-seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation_coarse=Multi-system&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, 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