metadata: run_metadata: 40 rows where experiment.library_selection = "other", technology = "unknown" and tissue_curation

40 rows where experiment.library_selection = "other", technology = "unknown" and tissue_curation_coarse = "Multi-system"

descending

Link	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.extractprotocol	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
9343	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	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	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 o…	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 incubati…	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	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 o…	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 incubati…	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	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 o…	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 incubati…	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	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 o…	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 incubati…	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	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 o…	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 incubati…	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	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 o…	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 incubati…	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;