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
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,,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 µM 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® 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,,,,,,,,,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. 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 µM 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® 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:0|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,Cnt-mRNA-ML-4_2.fastq.gz Cnt-mRNA-ML-4_1.fastq.gz,fastq fastq,12134105440.0,75838159.0,E MTAB 7464:Cnt mRNA ML 4 ,0:80 1:80,A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860,80,80,,,3262023701,2677095735,2964643096,3227367048,2975860,ERX2938586,ERS2922622,ERA1667271,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.91144,0.90945,0.31692,0.30691,0.75203,0.75722,0.51882,0.5197,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2018-11-28,Adult,Adult,Multi-tissue,Multi-system
9344,ERR2935791,ERX2938585,ERS2922621,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,,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 µM 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® 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,,,,,,,,,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. 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 µM 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® 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:0|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,Cnt-mRNA-ML-3_1.fastq.gz Cnt-mRNA-ML-3_2.fastq.gz,fastq fastq,10198941920.0,63743387.0,E MTAB 7464:Cnt mRNA ML 3 ,0:80 1:80,A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227,80,80,,,2707258482,2295053882,2521099885,2673029444,2500227,ERX2938585,ERS2922621,ERA1667271,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.88029,0.87951,0.30611,0.30513,0.76189,0.7685,0.52656,0.52076,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2018-11-28,Adult,Adult,Multi-tissue,Multi-system
9345,ERR2935790,ERX2938584,ERS2922620,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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:0|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,Cnt-mRNA-ML-2_1.fastq.gz Cnt-mRNA-ML-2_2.fastq.gz,fastq fastq,13001272960.0,81257956.0,E MTAB 7464:Cnt mRNA ML 2 ,0:80 1:80,A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729,80,80,,,3429977204,2902807573,3288394622,3376870832,3222729,ERX2938584,ERS2922620,ERA1667271,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.89439,0.89378,0.3049,0.30551,0.75771,0.76761,0.52718,0.52248,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2018-11-28,Adult,Adult,Multi-tissue,Multi-system
9346,ERR2935789,ERX2938583,ERS2922619,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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:0|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,Cnt-mRNA-ML-1_2.fastq.gz Cnt-mRNA-ML-1_1.fastq.gz,fastq fastq,10689399040.0,66808744.0,E MTAB 7464:Cnt mRNA ML 1 ,0:80 1:80,A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382,80,80,,,2897858681,2320332197,2613694217,2854881563,2632382,ERX2938583,ERS2922619,ERA1667271,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.87118,0.87075,0.30823,0.30776,0.74673,0.75692,0.49822,0.50666,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2018-11-28,Adult,Adult,Multi-tissue,Multi-system
9347,ERR2935788,ERX2938582,ERS2922618,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 µM 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® 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,,,,,,,,,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 µM 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® 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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,,,,,,,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 °C 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 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at 80 °C or RNA extraction was continued immediately by adding 140 µL 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 °C. 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 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. 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 °C 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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,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,,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 µM 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,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,,,,,,,,,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,,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,,,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,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,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.,,pubmed:32912962,,Adult tail 2,GSM4591062,,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,,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,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591062,GSM4591062: Adult tail 2; Danio rerio; OTHER,GSM4591062,,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,,SRP265951,,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,,,,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,,0.20653,,0.88722,,0.58074,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,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.,,pubmed:32912962,,Adult tail 1,GSM4591061,,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,,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,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591061,GSM4591061: Adult tail 1; Danio rerio; OTHER,GSM4591061,,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,,SRP265951,,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,,,,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,,0.12127,,0.91806,,0.67424,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Adult,Adult,Multi-tissue,Multi-system