metadata: run_metadata: 468 rows where devstage_curation_coarse = "Adult" and experiment.library

468 rows where devstage_curation_coarse = "Adult" and experiment.library_selection = "other"

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.treatmentprotocol	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
7949	7949	ERR015566	ERX005931	ERS000090	ERP000263	PRJEB2208	Zebrafish gene three prime end pull down for genome annotation	E-MTAB-308	Transcriptome Analysis					ZF ovary sample1	SAMEA708832	Wellcome Sanger Institute	Alias:ZF ovary sample1\|Description:RNA extracted from adult zebrafish ovary\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000090\|Sample Name:ERS000090\|Sex:female\|Strain:Tuebingen\|Title:Danio rerio								Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert	Zebrafish adult ovary mRNA three prime end	Zebrafish gene three prime end pull down for genome annotation	20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.	Experimental Factor: DEVELOPMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:ovary\|Experimental Factor: SEX:female	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000263	Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation	ENA FIRST PUBLIC:2010 08 19\|ENA LAST UPDATE:2018 11 16	3444_6.srf	srf	1150193272.0	7567061.0	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish ovary dpf three prime pull down paired end 250 to 300 bp insert	0:76 1:76	A:280621121;C:291623460;G:285422205;T:273609496;N:18916990	76	76	280621121	291623460	285422205	273609496	18916990	ERX005931	ERS000090	ERA010603	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.96663	0.96605	0.0126	0.01249	0.82272	0.82548	0.45602	0.45286	76	76	B	B	biological fallback assumption	illumina	early_illumina	3prime	other	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Gonad	Reproductive System
7950	7950	ERR015567	ERX005930	ERS000089	ERP000263	PRJEB2208	Zebrafish gene three prime end pull down for genome annotation	E-MTAB-308	Transcriptome Analysis				RNA extracted from male adult zebrafish head		SAMEA708835	SC	ENA FIRST PUBLIC:2010 02 26T10:44:13Z\|ENA LAST UPDATE:2018 03 08T15:51:30Z\|External Id:SAMEA708835\|INSDC center name:SC\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:51:30Z\|INSDC status:public\|Submitter Id:ZF male head sample1\|common name:zebrafish\|sample name:ZF male head sample1\|scientific name:Danio rerio\|sex:male\|strain:Tuebingen								Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert	Zebrafish adult male head mRNA three prime end	Zebrafish gene three prime end pull down for genome annotation	20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.	Experimental Factor: DEVELOPMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:head\|Experimental Factor: SEX:male	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000263	Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation	ENA FIRST PUBLIC:2010 08 19\|ENA LAST UPDATE:2018 11 16	3444_7.srf	srf	1384012896.0	9105348.0	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert	0:76 1:76	A:369912216;C:306963547;G:292249178;T:392053840;N:22834115	76	76	369912216	306963547	292249178	392053840	22834115	ERX005930	ERS000089	ERA010603	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.95932	0.96084	0.20719	0.21321	0.73959	0.74763	0.47227	0.48033	76	76	B	B	biological fallback assumption	illumina	early_illumina	3prime	other	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Head	Nervous System
7952	7952	ERR015568	ERX005928	ERS000087	ERP000263	PRJEB2208	Zebrafish gene three prime end pull down for genome annotation	E-MTAB-308	Transcriptome Analysis					ZF male sample1	SAMEA708829	Wellcome Sanger Institute	Alias:ZF male sample1\|Description:RNA extracted from whole male adult zebrafish without xxx\|INSDC center alias:SC\|INSDC center name:Wellcome Sanger Institute\|INSDC first public:2010 02 26T10:44:13Z\|INSDC last update:2018 03 08T15:24:37Z\|INSDC status:public\|SRA accession:ERS000087\|Sample Name:ERS000087\|Sex:male\|Strain:Tuebingen\|Title:Danio rerio								Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male body dpf three prime pull down paired end 250 to 300 bp insert	Zebrafish adult male body mRNA three prime end	Zebrafish gene three prime end pull down for genome annotation	20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.	Experimental Factor: DEVELOPMENTAL STAGE:adult\|Experimental Factor: ORGANISM PART:whole fish without xxx\|Experimental Factor: SEX:male	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina Genome Analyzer II		ERP000263	Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation	ENA FIRST PUBLIC:2010 08 19\|ENA LAST UPDATE:2018 11 16	3444_8.srf	srf	1012667320.0	6662285.0	E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male body dpf three prime pull down paired end 250 to 300 bp insert	0:76 1:76	A:262408681;C:234183204;G:228254982;T:271015871;N:16804582	76	76	262408681	234183204	228254982	271015871	16804582	ERX005928	ERS000087	ERA010603	SC\|Wellcome Trust Sanger Institute	SC\|Wellcome Trust Sanger Institute	2	0.95123	0.96116	0.23163	0.22276	0.77847	0.78648	0.42301	0.43528	76	76	B	B	biological fallback assumption	illumina	early_illumina	3prime	other	unknown	bulk	unknown	unknown	United Kingdom	2010-02-26	Adult	Adult	Whole Organism	All anatomical structures
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
9927	9927	ERR4321734	ERX4268592	ERS4808149	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni R 3	SAMEA7047515	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047515\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni R 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni R 3\|sampling site:right cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni R 3 p	Ctrl uni R 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_R_3_1.txt Ctrl_uni_R_3_2.txt	fastq fastq	7001062560.0	43756641.0	E MTAB 9321:Ctrl uni R 3	0:80 1:80	A:1691997382;C:1785031961;G:1794429141;T:1728559618;N:1044458	80	80	1691997382	1785031961	1794429141	1728559618	1044458	ERX4268592	ERS4808149	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93339	0.93586	0.30761	0.30942	0.77031	0.77285	0.6535	0.63203	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9928	9928	ERR4321733	ERX4268591	ERS4808148	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni R 2	SAMEA7047514	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047514\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni R 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni R 2\|sampling site:right cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni R 2 p	Ctrl uni R 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_R_2_1.txt Ctrl_uni_R_2_2.txt	fastq fastq	6922683200.0	43266770.0	E MTAB 9321:Ctrl uni R 2	0:80 1:80	A:1632897692;C:1799983634;G:1813073970;T:1675697152;N:1030752	80	80	1632897692	1799983634	1813073970	1675697152	1030752	ERX4268591	ERS4808148	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.9343	0.93678	0.30732	0.30767	0.77226	0.77496	0.67322	0.638	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9929	9929	ERR4321732	ERX4268590	ERS4808147	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni R 1	SAMEA7047513	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047513\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni R 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni R 1\|sampling site:right cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni R 1 p	Ctrl uni R 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_R_1_1.txt Ctrl_uni_R_1_2.txt	fastq fastq	7277767680.0	45486048.0	E MTAB 9321:Ctrl uni R 1	0:80 1:80	A:1716271935;C:1890805720;G:1910764817;T:1758823538;N:1101670	80	80	1716271935	1890805720	1910764817	1758823538	1101670	ERX4268590	ERS4808147	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93132	0.93607	0.29495	0.29694	0.77916	0.78023	0.66985	0.69546	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9930	9930	ERR4321731	ERX4268589	ERS4808146	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni L 3	SAMEA7047512	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047512\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni L 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni L 3\|sampling site:left cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni L 3 p	Ctrl uni L 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_L_3_1.txt Ctrl_uni_L_3_2.txt	fastq fastq	6575179520.0	41094872.0	E MTAB 9321:Ctrl uni L 3	0:80 1:80	A:1482672127;C:1776068618;G:1790187841;T:1525260758;N:990176	80	80	1482672127	1776068618	1790187841	1525260758	990176	ERX4268589	ERS4808146	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.94459	0.94749	0.2565	0.25972	0.77816	0.77881	0.67376	0.6469	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9931	9931	ERR4321730	ERX4268588	ERS4808145	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni L 2	SAMEA7047511	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047511\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni L 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni L 2\|sampling site:left cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni L 2 p	Ctrl uni L 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_L_2_1.txt Ctrl_uni_L_2_2.txt	fastq fastq	7275818080.0	45473863.0	E MTAB 9321:Ctrl uni L 2	0:80 1:80	A:1706173762;C:1899925486;G:1918514584;T:1750098284;N:1105964	80	80	1706173762	1899925486	1918514584	1750098284	1105964	ERX4268588	ERS4808145	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93448	0.93897	0.29227	0.29368	0.77299	0.77587	0.67483	0.69924	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9932	9932	ERR4321729	ERX4268587	ERS4808144	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni L 1	SAMEA7047510	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047510\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni L 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni L 1\|sampling site:left cerebral hemisphere\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni L 1 p	Ctrl uni L 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_L_1_1.txt Ctrl_uni_L_1_2.txt	fastq fastq	6259547520.0	39122172.0	E MTAB 9321:Ctrl uni L 1	0:80 1:80	A:1504594075;C:1603950703;G:1614410199;T:1535635583;N:956960	80	80	1504594075	1603950703	1614410199	1535635583	956960	ERX4268587	ERS4808144	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.92994	0.93276	0.31313	0.31395	0.77195	0.77372	0.66568	0.6882	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9933	9933	ERR4321728	ERX4268586	ERS4808143	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl uni 3	SAMEA7047509	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047509\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl uni 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl uni 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl uni 3 p	3dpl uni 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_uni_3_1.txt 3dpl_uni_3_2.txt	fastq fastq	7967977760.0	49799861.0	E MTAB 9321:3dpl uni 3	0:80 1:80	A:2260216672;C:1639328793;G:1824529883;T:2241676126;N:2226286	80	80	2260216672	1639328793	1824529883	2241676126	2226286	ERX4268586	ERS4808143	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.90526	0.90173	0.44801	0.44169	0.73827	0.74854	0.51874	0.52672	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9934	9934	ERR4321727	ERX4268585	ERS4808142	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl uni 2	SAMEA7047508	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047508\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl uni 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl uni 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl uni 2 p	3dpl uni 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_uni_2_1.txt 3dpl_uni_2_2.txt	fastq fastq	9215409600.0	57596310.0	E MTAB 9321:3dpl uni 2	0:80 1:80	A:2620502481;C:1914345031;G:2080364714;T:2597606056;N:2591318	80	80	2620502481	1914345031	2080364714	2597606056	2591318	ERX4268585	ERS4808142	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91412	0.91102	0.42824	0.4207	0.73091	0.73671	0.52094	0.52307	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9935	9935	ERR4321726	ERX4268584	ERS4808141	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl uni 1	SAMEA7047507	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047507\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl uni 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl uni 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl uni 1 p	3dpl uni 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_uni_1_1.txt 3dpl_uni_1_2.txt	fastq fastq	9713477280.0	60709233.0	E MTAB 9321:3dpl uni 1	0:80 1:80	A:2666518127;C:1984727973;G:2436235221;T:2623269258;N:2726701	80	80	2666518127	1984727973	2436235221	2623269258	2726701	ERX4268584	ERS4808141	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91468	0.89921	0.41764	0.40764	0.73403	0.74608	0.52391	0.52748	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9936	9936	ERR4321725	ERX4268583	ERS4808140	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl uni 3	SAMEA7047506	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047506\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl uni 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl uni 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl uni 3 p	20hpl uni 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_uni_3_1.txt 20hpl_uni_3_2.txt	fastq fastq	8675853280.0	54224083.0	E MTAB 9321:20hpl uni 3	0:80 1:80	A:2365631089;C:1890091876;G:2067595442;T:2325000100;N:27534773	80	80	2365631089	1890091876	2067595442	2325000100	27534773	ERX4268583	ERS4808140	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.90101	0.90675	0.42722	0.4249	0.74337	0.75294	0.51417	0.52085	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9937	9937	ERR4321724	ERX4268582	ERS4808139	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl uni 2	SAMEA7047505	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047505\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl uni 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl uni 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl uni 2 p	20hpl uni 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_uni_2_1.txt 20hpl_uni_2_2.txt	fastq fastq	4735091040.0	29594319.0	E MTAB 9321:20hpl uni 2	0:80 1:80	A:1061979324;C:1276598224;G:1297035795;T:1098757554;N:720143	80	80	1061979324	1276598224	1297035795	1098757554	720143	ERX4268582	ERS4808139	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.9384	0.94067	0.25644	0.25853	0.7877	0.78843	0.69474	0.72221	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9938	9938	ERR4321723	ERX4268581	ERS4808138	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl uni 1	SAMEA7047504	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047504\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl uni 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl uni 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl uni 1 p	20hpl uni 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_uni_1_1.txt 20hpl_uni_1_2.txt	fastq fastq	10122915040.0	63268219.0	E MTAB 9321:20hpl uni 1	0:80 1:80	A:2917523358;C:2094720604;G:2205586268;T:2872641443;N:32443367	80	80	2917523358	2094720604	2205586268	2872641443	32443367	ERX4268581	ERS4808138	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.90867	0.91132	0.46283	0.46241	0.74858	0.75357	0.53145	0.53522	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9939	9939	ERR4321722	ERX4268580	ERS4808137	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in IWR 3	SAMEA7047503	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047503\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in IWR 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in IWR 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in IWR 3 p	3dpl in IWR 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_IWR_3_1.txt 3dpl_in_IWR_3_2.txt	fastq fastq	9476807840.0	59230049.0	E MTAB 9321:3dpl in IWR 3	0:80 1:80	A:2639849526;C:1994343199;G:2238787041;T:2601193111;N:2634963	80	80	2639849526	1994343199	2238787041	2601193111	2634963	ERX4268580	ERS4808137	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91666	0.90016	0.41957	0.41098	0.72679	0.73596	0.52875	0.53529	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9940	9940	ERR4321721	ERX4268579	ERS4808136	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in IWR 2	SAMEA7047502	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047502\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in IWR 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in IWR 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in IWR 2 p	3dpl in IWR 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_IWR_2_1.txt 3dpl_in_IWR_2_2.txt	fastq fastq	7305898240.0	45661864.0	E MTAB 9321:3dpl in IWR 2	0:80 1:80	A:2035812198;C:1535985603;G:1714961805;T:2017139933;N:1998701	80	80	2035812198	1535985603	1714961805	2017139933	1998701	ERX4268579	ERS4808136	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91721	0.90787	0.40247	0.39455	0.72916	0.74097	0.52622	0.52732	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9941	9941	ERR4321720	ERX4268578	ERS4808135	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in IWR 1	SAMEA7047501	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047501\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in IWR 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in IWR 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in IWR 1 p	3dpl in IWR 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_IWR_1_1.txt 3dpl_in_IWR_1_2.txt	fastq fastq	5893946400.0	36837165.0	E MTAB 9321:3dpl in IWR 1	0:80 1:80	A:1170533263;C:1737932152;G:1758304403;T:1226290662;N:885920	80	80	1170533263	1737932152	1758304403	1226290662	885920	ERX4268578	ERS4808135	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.95436	0.95726	0.17474	0.17743	0.77031	0.7726	0.72793	0.73265	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9942	9942	ERR4321719	ERX4268577	ERS4808134	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in IWR 3	SAMEA7047500	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047500\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in IWR 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in IWR 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in IWR 3 p	20hpl in IWR 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_IWR_3_1.txt 20hpl_in_IWR_3_2.txt	fastq fastq	6198105920.0	38738162.0	E MTAB 9321:20hpl in IWR 3	0:80 1:80	A:1441128066;C:1626141975;G:1647720111;T:1482170340;N:945428	80	80	1441128066	1626141975	1647720111	1482170340	945428	ERX4268577	ERS4808134	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.94334	0.94604	0.2532	0.25458	0.75941	0.76086	0.66584	0.67193	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9943	9943	ERR4321718	ERX4268576	ERS4808133	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in IWR 2	SAMEA7047499	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047499\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in IWR 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in IWR 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in IWR 2 p	20hpl in IWR 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_IWR_2_1.txt 20hpl_in_IWR_2_2.txt	fastq fastq	8244868480.0	51530428.0	E MTAB 9321:20hpl in IWR 2	0:80 1:80	A:2326026663;C:1706321438;G:1913900194;T:2272224793;N:26395392	80	80	2326026663	1706321438	1913900194	2272224793	26395392	ERX4268576	ERS4808133	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91275	0.90955	0.44535	0.44255	0.74456	0.75298	0.53931	0.53823	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9944	9944	ERR4321717	ERX4268575	ERS4808132	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in IWR 1	SAMEA7047498	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047498\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in IWR 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in IWR 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in IWR 1 p	20hpl in IWR 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions 4 1 3 3a 4 7 7a Hexahydro 1 3 dioxo 4 7 methano 2H isoindol 2 yl N 8 quinolinyl Benzamide IWR 1 was added to fish water at 20 micromolar. Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:IWR 1\|Experimental Factor: dose:20\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_IWR_1_1.txt 20hpl_in_IWR_1_2.txt	fastq fastq	8946910240.0	55918189.0	E MTAB 9321:20hpl in IWR 1	0:80 1:80	A:2523280880;C:1876368998;G:2029673577;T:2489111763;N:28475022	80	80	2523280880	1876368998	2029673577	2489111763	28475022	ERX4268575	ERS4808132	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91067	0.90286	0.45601	0.44987	0.7335	0.74119	0.51443	0.51662	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9945	9945	ERR4321716	ERX4268574	ERS4808131	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in 3	SAMEA7047497	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047497\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in 3 p	3dpl in 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_3_1.txt 3dpl_in_3_2.txt	fastq fastq	9556572640.0	59728579.0	E MTAB 9321:3dpl in 3	0:80 1:80	A:2669191918;C:1902750470;G:2361798477;T:2620161228;N:2670547	80	80	2669191918	1902750470	2361798477	2620161228	2670547	ERX4268574	ERS4808131	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91175	0.89329	0.42236	0.413	0.72671	0.74156	0.52222	0.52828	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9946	9946	ERR4321715	ERX4268573	ERS4808130	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in 2	SAMEA7047496	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:28Z\|External Id:SAMEA7047496\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:28Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in 2 p	3dpl in 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_2_1.txt 3dpl_in_2_2.txt	fastq fastq	10848117120.0	67800732.0	E MTAB 9321:3dpl in 2	0:80 1:80	A:2935795866;C:2381506213;G:2652994352;T:2874780262;N:3040427	80	80	2935795866	2381506213	2652994352	2874780262	3040427	ERX4268573	ERS4808130	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91965	0.89867	0.42158	0.41268	0.73342	0.74249	0.56938	0.56978	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9947	9947	ERR4321714	ERX4268572	ERS4808129	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl in 1	SAMEA7047495	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:28Z\|External Id:SAMEA7047495\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:28Z\|INSDC status:public\|Submitter Id:E MTAB 9321:3dpl in 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:3dpl in 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:3dpl in 1 p	3dpl in 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	3dpl_in_1_1.txt 3dpl_in_1_2.txt	fastq fastq	12371488960.0	77321806.0	E MTAB 9321:3dpl in 1	0:80 1:80	A:3438091571;C:2664088451;G:2872543859;T:3393310483;N:3454596	80	80	3438091571	2664088451	2872543859	3393310483	3454596	ERX4268572	ERS4808129	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.92096	0.90884	0.39682	0.3843	0.72614	0.73401	0.53892	0.53838	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9948	9948	ERR4321713	ERX4268571	ERS4808128	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in 3	SAMEA7047494	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:28Z\|External Id:SAMEA7047494\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:28Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in 3\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in 3 p	20hpl in 3 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_3_1.txt 20hpl_in_3_2.txt	fastq fastq	10464739040.0	65404619.0	E MTAB 9321:20hpl in 3	0:80 1:80	A:2995469080;C:2169447356;G:2318878018;T:2947444090;N:33500496	80	80	2995469080	2169447356	2318878018	2947444090	33500496	ERX4268571	ERS4808128	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.9098	0.91109	0.46632	0.4653	0.74276	0.75077	0.51527	0.52148	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9949	9949	ERR4321712	ERX4268570	ERS4808127	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in 2	SAMEA7047493	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:28Z\|External Id:SAMEA7047493\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:28Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in 2\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in 2 p	20hpl in 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_2_1.txt 20hpl_in_2_2.txt	fastq fastq	8520377280.0	53252358.0	E MTAB 9321:20hpl in 2	0:80 1:80	A:2416849489;C:1735946163;G:1978475279;T:2361749789;N:27356560	80	80	2416849489	1735946163	1978475279	2361749789	27356560	ERX4268570	ERS4808127	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.91434	0.91	0.42899	0.42662	0.73917	0.74876	0.52201	0.51826	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
9950	9950	ERR4321711	ERX4268569	ERS4808126	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	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 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. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	20hpl in 1	SAMEA7047492	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:28Z\|External Id:SAMEA7047492\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:28Z\|INSDC status:public\|Submitter Id:E MTAB 9321:20hpl in 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:20hpl in 1\|scientific name:Danio rerio\|sex:male								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:20hpl in 1 p	20hpl in 1 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions DMSO was added to fish water Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: compound:dimethyl sulfoxide\|Experimental Factor: time:20	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	20hpl_in_1_1.txt 20hpl_in_1_2.txt	fastq fastq	7150452800.0	44690330.0	E MTAB 9321:20hpl in 1	0:80 1:80	A:1771803292;C:1779551247;G:1798541378;T:1799460160;N:1096723	80	80	1771803292	1779551247	1798541378	1799460160	1096723	ERX4268569	ERS4808126	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.92622	0.93038	0.35018	0.35291	0.7727	0.77396	0.64402	0.65297	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2020-07-06	Adult	Adult	Brain	Nervous System
10324	10324	ERR7384926	ERX6953430	ERS8736631	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl 5	SAMEA11086968	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086968\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:Ctrl 5\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:telencephalon\|sample name:E MTAB 11163:Ctrl 5\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:Ctrl 5 p	Ctrl 5 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	Ctrl-5_1.fastq.gz Ctrl-5_2.fastq.gz	fastq fastq	7836077760.0	48975486.0	E MTAB 11163:Ctrl 5	0:80 1:80	A:2197807782;C:1719033269;G:1762364798;T:2156195280;N:676631	80	80	2197807782	1719033269	1762364798	2156195280	676631	ERX6953430	ERS8736631	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93458	0.93849	0.19317	0.18598	0.72855	0.72784	0.48113	0.4814	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10325	10325	ERR7384925	ERX6953429	ERS8736630	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl 4	SAMEA11086967	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086967\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:Ctrl 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:telencephalon\|sample name:E MTAB 11163:Ctrl 4\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:Ctrl 4 p	Ctrl 4 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	Ctrl-4_1.fastq.gz Ctrl-4_2.fastq.gz	fastq fastq	11841052800.0	74006580.0	E MTAB 11163:Ctrl 4	0:80 1:80	A:3269511229;C:2469072822;G:2920921930;T:3177156542;N:4390277	80	80	3269511229	2469072822	2920921930	3177156542	4390277	ERX6953429	ERS8736630	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.86759	0.86792	0.43044	0.42689	0.75469	0.76717	0.55291	0.55788	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10326	10326	ERR7384924	ERX6953428	ERS8736629	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl 3	SAMEA11086966	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086966\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:Ctrl 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:telencephalon\|sample name:E MTAB 11163:Ctrl 3\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:Ctrl 3 p	Ctrl 3 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	Ctrl-3_1.fastq.gz Ctrl-3_2.fastq.gz	fastq fastq	14286470240.0	89290439.0	E MTAB 11163:Ctrl 3	0:80 1:80	A:3956940377;C:3071545407;G:3372465520;T:3880155204;N:5363732	80	80	3956940377	3071545407	3372465520	3880155204	5363732	ERX6953428	ERS8736629	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.87493	0.87449	0.43889	0.44065	0.7541	0.76402	0.5369	0.53575	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10327	10327	ERR7384923	ERX6953427	ERS8736628	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl 2	SAMEA11086965	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086965\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:Ctrl 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:telencephalon\|sample name:E MTAB 11163:Ctrl 2\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:Ctrl 2 p	Ctrl 2 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	Ctrl-2_1.fastq.gz Ctrl-2_2.fastq.gz	fastq fastq	13169862240.0	82311639.0	E MTAB 11163:Ctrl 2	0:80 1:80	A:3683560119;C:2823399426;G:3030116974;T:3627855699;N:4930022	80	80	3683560119	2823399426	3030116974	3627855699	4930022	ERX6953427	ERS8736628	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.86757	0.87095	0.44548	0.45008	0.75536	0.76343	0.53366	0.54558	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10328	10328	ERR7384922	ERX6953426	ERS8736627	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl 1	SAMEA11086964	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086964\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:Ctrl 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|organism part:telencephalon\|sample name:E MTAB 11163:Ctrl 1\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:Ctrl 1 p	Ctrl 1 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	Ctrl-1_1.fastq.gz Ctrl-1_2.fastq.gz	fastq fastq	11349398560.0	70933741.0	E MTAB 11163:Ctrl 1	0:80 1:80	A:3132234873;C:2275439795;G:2903048149;T:3034427880;N:4247863	80	80	3132234873	2275439795	2903048149	3034427880	4247863	ERX6953426	ERS8736627	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.86563	0.85769	0.45807	0.45717	0.75542	0.76999	0.53285	0.52788	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10329	10329	ERR7384921	ERX6953425	ERS8736626	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl 4	SAMEA11086962	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086962\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:3dpl 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:3dpl 4\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:3dpl 4 p	3dpl 4 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	3dpl-4_1.fastq.gz 3dpl-4_2.fastq.gz	fastq fastq	12269133600.0	76682085.0	E MTAB 11163:3dpl 4	0:80 1:80	A:3308670822;C:2612099729;G:3097254260;T:3246547111;N:4561678	80	80	3308670822	2612099729	3097254260	3246547111	4561678	ERX6953425	ERS8736626	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.88949	0.88423	0.41382	0.41463	0.73856	0.75209	0.54087	0.53814	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10330	10330	ERR7384920	ERX6953424	ERS8736625	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl 3	SAMEA11086961	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086961\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:3dpl 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:3dpl 3\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:3dpl 3 p	3dpl 3 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	3dpl-3_1.fastq.gz 3dpl-3_2.fastq.gz	fastq fastq	12561832800.0	78511455.0	E MTAB 11163:3dpl 3	0:80 1:80	A:3518655485;C:2691495460;G:2879365772;T:3467606057;N:4710026	80	80	3518655485	2691495460	2879365772	3467606057	4710026	ERX6953424	ERS8736625	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.86128	0.86324	0.43991	0.44309	0.73998	0.74761	0.5283	0.52762	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10331	10331	ERR7384919	ERX6953423	ERS8736624	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl 2	SAMEA11086960	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086960\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:3dpl 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:3dpl 2\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:3dpl 2 p	3dpl 2 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	3dpl-2_1.fastq.gz 3dpl-2_2.fastq.gz	fastq fastq	12727937600.0	79549610.0	E MTAB 11163:3dpl 2	0:80 1:80	A:3511550580;C:2718113416;G:3063150762;T:3430381211;N:4741631	80	80	3511550580	2718113416	3063150762	3430381211	4741631	ERX6953423	ERS8736624	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.88126	0.88294	0.42008	0.41964	0.72687	0.73811	0.52924	0.52812	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10332	10332	ERR7384918	ERX6953422	ERS8736623	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	3dpl 1	SAMEA11086959	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086959\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:3dpl 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:3dpl 1\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:3dpl 1 p	3dpl 1 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:3	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	3dpl-1_1.fastq.gz 3dpl-1_2.fastq.gz	fastq fastq	10910301440.0	68189384.0	E MTAB 11163:3dpl 1	0:80 1:80	A:2970902938;C:2403780256;G:2602413517;T:2929186974;N:4017755	80	80	2970902938	2403780256	2602413517	2929186974	4017755	ERX6953422	ERS8736623	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.84003	0.84172	0.34597	0.34824	0.71589	0.72466	0.52558	0.52286	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10333	10333	ERR7384917	ERX6953421	ERS8736622	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	1dpl 5	SAMEA11086958	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086958\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:1dpl 5\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:1dpl 5\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:1dpl 5 p	1dpl 5 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	1dpl-5_1.fastq.gz 1dpl-5_2.fastq.gz	fastq fastq	10425544320.0	65159652.0	E MTAB 11163:1dpl 5	0:80 1:80	A:3050099743;C:2153241581;G:2229178430;T:2992123587;N:900979	80	80	3050099743	2153241581	2229178430	2992123587	900979	ERX6953421	ERS8736622	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.92853	0.93189	0.23718	0.23074	0.72366	0.72052	0.49924	0.511	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10334	10334	ERR7384916	ERX6953420	ERS8736621	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	1dpl 4	SAMEA11086957	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086957\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:1dpl 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:1dpl 4\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:1dpl 4 p	1dpl 4 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	1dpl-4_1.fastq.gz 1dpl-4_2.fastq.gz	fastq fastq	9244695360.0	57779346.0	E MTAB 11163:1dpl 4	0:80 1:80	A:2617398368;C:2006695457;G:2057821797;T:2561969157;N:810581	80	80	2617398368	2006695457	2057821797	2561969157	810581	ERX6953420	ERS8736621	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93687	0.94089	0.20045	0.19324	0.71674	0.71506	0.49841	0.50035	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10335	10335	ERR7384915	ERX6953419	ERS8736620	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	1dpl 3	SAMEA11086956	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086956\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:1dpl 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:1dpl 3\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:1dpl 3 p	1dpl 3 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	1dpl-3_1.fastq.gz 1dpl-3_2.fastq.gz	fastq fastq	9373333280.0	58583333.0	E MTAB 11163:1dpl 3	0:80 1:80	A:2671556387;C:2008711931;G:2062635156;T:2629594613;N:835193	80	80	2671556387	2008711931	2062635156	2629594613	835193	ERX6953419	ERS8736620	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93438	0.93842	0.21075	0.20463	0.71459	0.71246	0.50094	0.50105	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10336	10336	ERR7384914	ERX6953418	ERS8736619	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	1dpl 2	SAMEA11086955	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086955\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:1dpl 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:1dpl 2\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:1dpl 2 p	1dpl 2 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	1dpl-2_1.fastq.gz 1dpl-2_2.fastq.gz	fastq fastq	9647031680.0	60293948.0	E MTAB 11163:1dpl 2	0:80 1:80	A:2807310022;C:2016751282;G:2080246249;T:2741889329;N:834798	80	80	2807310022	2016751282	2080246249	2741889329	834798	ERX6953418	ERS8736619	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.92564	0.92819	0.22329	0.21583	0.72028	0.71877	0.50128	0.50045	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10337	10337	ERR7384913	ERX6953417	ERS8736618	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	1dpl 1	SAMEA11086954	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086954\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:1dpl 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:1dpl 1\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:1dpl 1 p	1dpl 1 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	1dpl-1_1.fastq.gz 1dpl-1_2.fastq.gz	fastq fastq	10054666560.0	62841666.0	E MTAB 11163:1dpl 1	0:80 1:80	A:2921800431;C:2104003276;G:2166908855;T:2861086535;N:867463	80	80	2921800431	2104003276	2166908855	2861086535	867463	ERX6953417	ERS8736618	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.93251	0.9361	0.22525	0.21776	0.71806	0.71478	0.5039	0.50925	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10338	10338	ERR7384912	ERX6953416	ERS8736617	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	14dpl 4	SAMEA11086953	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086953\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:14dpl 4\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:14dpl 4\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:14dpl 4 p	14dpl 4 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:14	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	14dpl-4_1.fastq.gz 14dpl-4_2.fastq.gz	fastq fastq	10510375520.0	65689847.0	E MTAB 11163:14dpl 4	0:80 1:80	A:2894001008;C:2230656231;G:2530263174;T:2852841235;N:2613872	80	80	2894001008	2230656231	2530263174	2852841235	2613872	ERX6953416	ERS8736617	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.8951	0.89119	0.46407	0.46205	0.74349	0.75043	0.52432	0.52127	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10339	10339	ERR7384911	ERX6953415	ERS8736616	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	14dpl 3	SAMEA11086952	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086952\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:14dpl 3\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:14dpl 3\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:14dpl 3 p	14dpl 3 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:14	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	14dpl-3_1.fastq.gz 14dpl-3_2.fastq.gz	fastq fastq	12643445600.0	79021535.0	E MTAB 11163:14dpl 3	0:80 1:80	A:3542554562;C:2679505652;G:2918520292;T:3499712681;N:3152413	80	80	3542554562	2679505652	2918520292	3499712681	3152413	ERX6953415	ERS8736616	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.90044	0.9018	0.4852	0.48223	0.75022	0.7557	0.52769	0.50719	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10340	10340	ERR7384910	ERX6953414	ERS8736615	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	14dpl 2	SAMEA11086951	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086951\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:14dpl 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:14dpl 2\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:14dpl 2 p	14dpl 2 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:14	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	14dpl-2_1.fastq.gz 14dpl-2_2.fastq.gz	fastq fastq	23194452640.0	144965329.0	E MTAB 11163:14dpl 2	0:80 1:80	A:6438735597;C:4960360012;G:5452621343;T:6336943660;N:5792028	80	80	6438735597	4960360012	5452621343	6336943660	5792028	ERX6953414	ERS8736615	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.90763	0.89955	0.47238	0.46518	0.7446	0.75544	0.5513	0.5514	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous System
10341	10341	ERR7384909	ERX6953413	ERS8736614	ERP133301	PRJEB48872	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	E-MTAB-11163	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 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. In this study we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing 1 day post lesion early proliferative 3 day post lesion and differentiation 14 day post lesion stages of regeneration.	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	14dpl 1	SAMEA11086950	Izmir Biomedicine and Genome Center	ENA first public:2022 01 31\|ENA last update:2022 01 31\|External Id:SAMEA11086950\|INSDC center alias:Izmir Biomedicine and Genome Center\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2022 01 31T00:14:07Z\|INSDC last update:2022 01 31T00:14:07Z\|INSDC status:public\|Submitter Id:E MTAB 11163:14dpl 1\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|injury:stab lesion\|organism part:telencephalon\|sample name:E MTAB 11163:14dpl 1\|sex:male\|strain:AB								NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the 3 different stages of the regenerating zebrafish telencephalon	E MTAB 11163:14dpl 1 p	14dpl 1 p	Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:stab lesion\|Experimental Factor: time:14	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP133301	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon	ENA FIRST PUBLIC:2022 01 31\|ENA LAST UPDATE:2022 01 31	14dpl-1_1.fastq.gz 14dpl-1_2.fastq.gz	fastq fastq	9754805920.0	60967537.0	E MTAB 11163:14dpl 1	0:80 1:80	A:2682345750;C:2040914324;G:2394726385;T:2634385060;N:2434401	80	80	2682345750	2040914324	2394726385	2634385060	2434401	ERX6953413	ERS8736614	ERA7396457	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.89908	0.89179	0.47056	0.46838	0.74231	0.7543	0.52672	0.52558	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown	Turkey	2022-01-31	Adult	Adult	Brain	Nervous 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
28725	28725	SRR26623262	SRX22323921	SRS19374450	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 cirbpb scars	GSM7875190		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 cirbpb scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875190	GSM7875190: Lineage tracing rep1 cirbpb scars; Danio rerio; OTHER	GSM7875190 r1	GSM7875190	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz	fastq fastq	157576336.0	949552.0	GSM7875190 r1										SRX22323921	SRS19374450	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00141	0.78069	0.00053	0.00877	0.99857	0.97822	0.33536	0.05199	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28726	28726	SRR26623263	SRX22323920	SRS19374449	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 cfl1 scars	GSM7875189		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 cfl1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875189	GSM7875189: Lineage tracing rep1 cfl1 scars; Danio rerio; OTHER	GSM7875189 r1	GSM7875189	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz	fastq fastq	381453696.0	2184402.0	GSM7875189 r1										SRX22323920	SRS19374449	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.0002	0.91626	0.00014	0.00132	0.99987	0.99726	0.16666	0.56363	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28727	28727	SRR26623264	SRX22323919	SRS19374448	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 actb2 scars	GSM7875188		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 actb2 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875188	GSM7875188: Lineage tracing rep1 actb2 scars; Danio rerio; OTHER	GSM7875188 r1	GSM7875188	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz	fastq fastq	491682118.0	2851156.0	GSM7875188 r1										SRX22323919	SRS19374448	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00051	0.41901	0.00032	0.0029	0.99945	0.99182	0.57575	0.007	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28728	28728	SRR26623265	SRX22323918	SRS19374446	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 actb1 scars	GSM7875187		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 actb1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875187	GSM7875187: Lineage tracing rep1 actb1 scars; Danio rerio; OTHER	GSM7875187 r1	GSM7875187	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz	fastq fastq	390405832.0	2283319.0	GSM7875187 r1										SRX22323918	SRS19374446	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00038	0.73548	0.00017	0.00057	0.99963	0.99571	0.29729	0.00243	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28729	28729	SRR26623266	SRX22323917	SRS19374447	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Brain 23 telencephalon Notch inhibition scSLAMseq	GSM7875186		source name:adult brain\|tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Notch inhibition DAPT\|geo loc name:missing\|collection date:missing	Brain 23 telencephalon Notch inhibition scSLAMseq	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq	adult brain	Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT Gamma Secretase Inhibitor Sigma Aldrich for 48 hours.	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …	tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Notch inhibition DAPT	GSM7875186	GSM7875186: Brain 23 telencephalon Notch inhibition scSLAMseq; Danio rerio; OTHER	GSM7875186 r1	GSM7875186	1	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz	fastq fastq	62392458570.0	271271559.0	GSM7875186 r1	0:28 1:202	A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393	28	202	18682905645	13783082970	14751373116	15161083446	14013393	SRX22323917	SRS19374447	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.01404	0.82351	0.00466	0.1026	0.99129	0.86774	0.36033	0.67345	28	202	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28730	28730	SRR26623267	SRX22323916	SRS19374445	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Brain 22 telencephalon control scSLAMseq	GSM7875185		source name:adult brain\|tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Control DMSO\|geo loc name:missing\|collection date:missing	Brain 22 telencephalon control scSLAMseq	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq	adult brain	Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …	tissue:adult brain\|tissue region:telencephalon\|cell type:mixed tissue dissociation\|genotype:wildtype\|treatment:Control DMSO	GSM7875185	GSM7875185: Brain 22 telencephalon control scSLAMseq; Danio rerio; OTHER	GSM7875185 r1	GSM7875185	1	The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions …		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz	fastq fastq	59793114490.0	259970063.0	GSM7875185 r1	0:28 1:202	A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613	28	202	18600519530	12714987967	14147370465	14316863915	13372613	SRX22323916	SRS19374445	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.01402	0.79448	0.00498	0.11405	0.99074	0.8518	0.39874	0.67082	28	202	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28754	28754	SRR26623291	SRX22323897	SRS19374426	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep2 ube2e1 scars	GSM7875196		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 ube2e1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875196	GSM7875196: Lineage tracing rep2 ube2e1 scars; Danio rerio; OTHER	GSM7875196 r1	GSM7875196	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz	fastq fastq	213092161.0	1190459.0	GSM7875196 r1										SRX22323897	SRS19374426	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00752	0.90776	0.00286	0.01739	0.99346	0.95444	0.46002	0.96817	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28755	28755	SRR26623292	SRX22323896	SRS19374425	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep2 rpl39 scars	GSM7875195		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 rpl39 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875195	GSM7875195: Lineage tracing rep2 rpl39 scars; Danio rerio; OTHER	GSM7875195 r1	GSM7875195	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz	fastq fastq	1023403502.0	5717338.0	GSM7875195 r1										SRX22323896	SRS19374425	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00086	0.83744	0.0003	0.00337	0.99845	0.97057	0.26605	0.40241	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28756	28756	SRR26623293	SRX22323895	SRS19374424	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep2 cirbpb scars	GSM7875194		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 cirbpb scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875194	GSM7875194: Lineage tracing rep2 cirbpb scars; Danio rerio; OTHER	GSM7875194 r1	GSM7875194	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz	fastq fastq	276120388.0	1542572.0	GSM7875194 r1										SRX22323895	SRS19374424	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00206	0.80328	0.00078	0.00662	0.9975	0.98039	0.55421	0.0258	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28757	28757	SRR26623294	SRX22323894	SRS19374423	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep2 cfl1 scars	GSM7875193		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep2 cfl1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875193	GSM7875193: Lineage tracing rep2 cfl1 scars; Danio rerio; OTHER	GSM7875193 r1	GSM7875193	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469552		loader:fastq load.py	lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz	fastq fastq	791318009.0	4420771.0	GSM7875193 r1										SRX22323894	SRS19374423	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00067	0.46079	0.00055	0.16353	0.99965	0.99332	0.52631	0.44939	28	151	T	B	sc-like readlen	illumina	novaseq_era	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28758	28758	SRR26623295	SRX22323893	SRS19374421	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 ube2e1 scars	GSM7875192		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 ube2e1 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875192	GSM7875192: Lineage tracing rep1 ube2e1 scars; Danio rerio; OTHER	GSM7875192 r1	GSM7875192	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz	fastq fastq	99407618.0	601781.0	GSM7875192 r1										SRX22323893	SRS19374421	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00657	0.84532	0.00205	0.03049	0.99537	0.95286	0.43306	0.19203	28	150	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
28759	28759	SRR26623296	SRX22323892	SRS19374422	SRP469552	PRJNA1034159	Dissecting the spatiotemporal diversity of adult neural stem cells	GSE246714	Other	Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.		pubmed:38365956		Lineage tracing rep1 rpl39 scars	GSM7875191		source name:adult brain\|tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]\|geo loc name:missing\|collection date:missing	Lineage tracing rep1 rpl39 scars	The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.	adult brain		Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.	tissue:adult brain\|cell type:mixed tissue dissociation\|genotype:Tg[ubi:zebrabow M]	GSM7875191	GSM7875191: Lineage tracing rep1 rpl39 scars; Danio rerio; OTHER	GSM7875191 r1	GSM7875191	1	Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform.		OTHER	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		SRP469552		loader:fastq load.py	lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz	fastq fastq	401898718.0	2276836.0	GSM7875191 r1										SRX22323892	SRS19374422	SRA1743007	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine	2	0.00037	0.2642	0.00015	0.00086	0.99922	0.99026	0.23076	0.42455	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	other	unknown	sc	single_cell_droplet	10x	Germany	2023-10-31	Adult	Adult	Brain	Nervous System
32508	32508	SRR29290248	SRX24807391	SRS21522263	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			15 days experimental group parallel 1	liver transcriptome	L4 1		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L4 1	L4 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TMFA6-7L.R1.fq.gz TMFA6-7L.R2.fq.gz	fastq fastq	5892231600.0	19640772.0	TMFA6 7L.R1.fq.gz	0:150 1:150	A:1471743634;C:1450664701;G:1502453832;T:1466956960;N:412473	150	150	1471743634	1450664701	1502453832	1466956960	412473	SRX24807391	SRS21522263	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32509	32509	SRR29290249	SRX24807390	SRS21522262	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 3	liver transcriptome	L3 3		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L3 3	L3 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLSC-5L.R1.fq.gz TLSC-5L.R2.fq.gz	fastq fastq	6269295000.0	20897650.0	TLSC 5L.R1.fq.gz	0:150 1:150	A:1541736942;C:1578334203;G:1620160556;T:1528907120;N:156179	150	150	1541736942	1578334203	1620160556	1528907120	156179	SRX24807390	SRS21522262	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32510	32510	SRR29290250	SRX24807389	SRS21522261	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 2	liver transcriptome	L3 2		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L3 2	L3 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLSB-3L.R1.fq.gz TLSB-3L.R2.fq.gz	fastq fastq	6206673000.0	20688910.0	TLSB 3L.R1.fq.gz	0:150 1:150	A:1592564670;C:1487253074;G:1531600191;T:1595004475;N:250590	150	150	1592564670	1487253074	1531600191	1595004475	250590	SRX24807389	SRS21522261	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32511	32511	SRR29290251	SRX24807388	SRS21522260	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 1	liver transcriptome	L3 1		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L3 1	L3 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLSA-1L.R1.fq.gz TLSA-1L.R2.fq.gz	fastq fastq	6188928300.0	20629761.0	TLSA 1L.R1.fq.gz	0:150 1:150	A:1584479312;C:1464260894;G:1549296685;T:1590644766;N:246643	150	150	1584479312	1464260894	1549296685	1590644766	246643	SRX24807388	SRS21522260	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32512	32512	SRR29290252	SRX24807387	SRS21522259	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			15 days experimental group parallel 3	liver transcriptome	L2 3		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L2 3	L2 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLFC1-3L.R1.fq.gz TLFC1-3L.R2.fq.gz	fastq fastq	6367070400.0	21223568.0	TLFC1 3L.R1.fq.gz	0:150 1:150	A:1579430230;C:1587605262;G:1613210542;T:1586578782;N:245584	150	150	1579430230	1587605262	1613210542	1586578782	245584	SRX24807387	SRS21522259	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32513	32513	SRR29290253	SRX24807386	SRS21522258	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			15 days experimental group parallel 2	liver transcriptome	L2 2		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L2 2	L2 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLFB1-3L.R1.fq.gz TLFB1-3L.R2.fq.gz	fastq fastq	6996653100.0	23322177.0	TLFB1 3L.R1.fq.gz	0:150 1:150	A:1803878205;C:1678057588;G:1715367000;T:1799170285;N:180022	150	150	1803878205	1678057588	1715367000	1799170285	180022	SRX24807386	SRS21522258	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32514	32514	SRR29290254	SRX24807385	SRS21522257	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			15 days experimental group parallel 1	liver transcriptome	L2 1		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L2 1	L2 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TLFA6-7L.R1.fq.gz TLFA6-7L.R2.fq.gz	fastq fastq	6109509300.0	20365031.0	TLFA6 7L.R1.fq.gz	0:150 1:150	A:1525902154;C:1507317327;G:1549698641;T:1526193716;N:397462	150	150	1525902154	1507317327	1549698641	1526193716	397462	SRX24807385	SRS21522257	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32515	32515	SRR29290255	SRX24807384	SRS21522256	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 3	liver transcriptome	L7 3		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L7 3	L7 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TSSC-5L.R1.fq.gz TSSC-5L.R2.fq.gz	fastq fastq	6846271200.0	22820904.0	TSSC 5L.R1.fq.gz	0:150 1:150	A:1704275603;C:1639794530;G:1792628691;T:1709317043;N:255333	150	150	1704275603	1639794530	1792628691	1709317043	255333	SRX24807384	SRS21522256	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32516	32516	SRR29290256	SRX24807383	SRS21522255	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			Control parallel 3	liver transcriptome	L1 3		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal								Zebrafish liver	L1 3	L1 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			FCFC1-3L.R1.fq.gz FCFC1-3L.R2.fq.gz	fastq fastq	6360438000.0	21201460.0	FCFC1 3L.R1.fq.gz	0:150 1:150	A:1591177652;C:1544470038;G:1615057708;T:1609485267;N:247335	150	150	1591177652	1544470038	1615057708	1609485267	247335	SRX24807383	SRS21522255	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32517	32517	SRR29290257	SRX24807382	SRS21522254	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 2	liver transcriptome	L7 2		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L7 2	L7 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TSSB-3L.R1.fq.gz TSSB-3L.R2.fq.gz	fastq fastq	6285285600.0	20950952.0	TSSB 3L.R1.fq.gz	0:150 1:150	A:1584093051;C:1516123512;G:1599998121;T:1584824364;N:246552	150	150	1584093051	1516123512	1599998121	1584824364	246552	SRX24807382	SRS21522254	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32518	32518	SRR29290258	SRX24807381	SRS21522253	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles			30 days experimental group parallel 1	liver transcriptome	L7 1		strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal								Zebrafish liver	L7 1	L7 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.			OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901			TSSA-1L.R1.fq.gz TSSA-1L.R2.fq.gz	fastq fastq	6078740100.0	20262467.0	TSSA 1L.R1.fq.gz	0:150 1:150	A:1530149533;C:1486474895;G:1528868563;T:1533006599;N:240510	150	150	1530149533	1486474895	1528868563	1533006599	240510	SRX24807381	SRS21522253	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary 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");;