rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
7946,ERR015563,ERX005934,ERS012707,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,E MTAB 308:Zebrafish embryo 2 dpf 2,SAMEA898403,Wellcome Sanger Institute,Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine: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 Zebrafish embryo 2 dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish embro 2 dpf 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: AGE:2 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex,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_2.srf,srf,990308120.0,6515185.0,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 2 dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:279665076;C:200433201;G:189692111;T:304366697;N:16151035,76,76,,,279665076,200433201,189692111,304366697,16151035,ERX005934,ERS012707,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.93964,0.94008,0.40095,0.39969,0.74424,0.74915,0.49535,0.49761,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Hatching,Embryo,Whole Organism,All anatomical structures
7947,ERR015564,ERX005933,ERS012706,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,E MTAB 308:Zebrafish embryo 3 dpf 2,SAMEA898404,Wellcome Sanger Institute,Age:3 days|Alias:E MTAB 308:Zebrafish embryo 3 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012706|Sample Name:ERS012706|Sex:unknown sex|StrainOrLine: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 Zebrafish embryo 3 dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish embro 3 dpf 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: AGE:3 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex,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_3.srf,srf,1572215648.0,10343524.0,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 3 dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:395189954;C:374281517;G:356666372;T:420372888;N:25704917,76,76,,,395189954,374281517,356666372,420372888,25704917,ERX005933,ERS012706,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.96337,0.96626,0.12558,0.12974,0.7824,0.79086,0.40731,0.41802,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
7948,ERR015562,ERX005932,ERS012705,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,E MTAB 308:Zebrafish embryo 1 dpf 2,SAMEA898401,Wellcome Sanger Institute,Age:1 days|Alias:E MTAB 308:Zebrafish embryo 1 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012705|Sample Name:ERS012705|Sex:unknown sex|StrainOrLine: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 Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish embro 1 dpf 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: AGE:1 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex,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_1.srf,srf,1358041568.0,8934484.0,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 1 dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:376045982;C:281568469;G:271365867;T:407279179;N:21782071,76,76,,,376045982,281568469,271365867,407279179,21782071,ERX005932,ERS012705,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.94607,0.94542,0.3002,0.30139,0.73584,0.74038,0.51058,0.51233,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
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,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
7951,ERR015565,ERX005929,ERS012704,ERP000263,PRJEB2208,Zebrafish gene three prime end pull down for genome annotation,E-MTAB-308,Transcriptome Analysis,,,,,E MTAB 308:Zebrafish embryo 5 dpf 2,SAMEA980815,SC,Age:5 days|Alias:E MTAB 308:Zebrafish embryo 5 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at  70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center name:SC|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012704|Sample Name:ERS012704|Sex:unknown sex|StrainOrLine: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 Zebrafish embryo 5 dpf three prime pull down paired end 250 to 300 bp insert,Zebrafish embro 5 dpf 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: AGE:5 d|Experimental Factor: DEVELOPMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism|Experimental Factor: SEX:unknown sex,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_5.srf,srf,1399629832.0,9208091.0,E MTAB 308:Illumina Genome Analyzer II sequencing of Zebrafish embryo 5 dpf three prime pull down paired end 250 to 300 bp insert,0:76 1:76,A:389123080;C:293319124;G:279736391;T:414876632;N:22574605,76,76,,,389123080,293319124,279736391,414876632,22574605,ERX005929,ERS012704,ERA010603,SC|Wellcome Trust Sanger Institute,SC|Wellcome Trust Sanger Institute,2,0.92999,0.9332,0.45309,0.46162,0.72419,0.73919,0.49892,0.50512,76,76,B,B,biological fallback assumption,illumina,early_illumina,3prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2010-08-19,Larval,Larval,Whole Organism,All anatomical structures
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
9337,ERR2865439,ERX2871399,ERS2871019,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,sibling 3,SAMEA5059848,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059848|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling3|common name:zebrafish|sample name:ele sibling3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_sib_F_CTTGTA_L004_R2_001.fastq.gz ele_sib_F_CTTGTA_L004_R1_001.fastq.gz,fastq fastq,2823621200.0,14118106.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6,0:100 1:100,A:752781583;C:663838191;G:656422705;T:750213027;N:365694,100,100,,,752781583,663838191,656422705,750213027,365694,ERX2871399,ERS2871019,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.95595,0.95486,0.09407,0.09431,0.67529,0.67673,0.45173,0.44515,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
9338,ERR2865438,ERX2871398,ERS2871018,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,sibling 2,SAMEA5059847,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059847|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling2|common name:zebrafish|sample name:ele sibling2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_sib_D_GCCAAT_L004_R1_001.fastq.gz ele_sib_D_GCCAAT_L004_R2_001.fastq.gz,fastq fastq,4217962600.0,21089813.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5,0:100 1:100,A:1119324653;C:996982862;G:984906708;T:1116209552;N:538825,100,100,,,1119324653,996982862,984906708,1116209552,538825,ERX2871398,ERS2871018,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.95341,0.95274,0.09215,0.09238,0.67296,0.67493,0.46185,0.4648,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
9339,ERR2865437,ERX2871397,ERS2871017,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,sibling 1,SAMEA5059846,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz,fastq fastq,5241628000.0,26208140.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4,0:100 1:100,A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601,100,100,,,1393802799,1235804455,1219328189,1392021956,670601,ERX2871397,ERS2871017,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.95296,0.95133,0.10275,0.1028,0.67018,0.67146,0.46488,0.46482,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
9340,ERR2865436,ERX2871396,ERS2871016,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,mutant3,SAMEA5059845,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059845|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant3|common name:zebrafish|sample name:ele mutant3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_E_CAGATC_L004_R1_001.fastq.gz ele_E_CAGATC_L004_R2_001.fastq.gz,fastq fastq,3529752000.0,17648760.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3,0:100 1:100,A:933354224;C:837396695;G:828677816;T:929860782;N:462483,100,100,,,933354224,837396695,828677816,929860782,462483,ERX2871396,ERS2871016,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.95621,0.95302,0.08584,0.08536,0.67048,0.67146,0.46615,0.46682,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
9341,ERR2865435,ERX2871395,ERS2871015,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,mutant2,SAMEA5059844,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059844|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant2|common name:zebrafish|sample name:ele mutant2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_C_ACAGTG_L004_R1_001.fastq.gz ele_C_ACAGTG_L004_R2_001.fastq.gz,fastq fastq,3119723800.0,15598619.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2,0:100 1:100,A:828335602;C:736691663;G:727853394;T:826449133;N:394008,100,100,,,828335602,736691663,727853394,826449133,394008,ERX2871395,ERS2871015,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.94967,0.94864,0.0992,0.09955,0.65928,0.66014,0.47042,0.46835,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
9342,ERR2865434,ERX2871394,ERS2871014,ERP111778,PRJEB29472,RNAseq analysis of slbp mutants in Zebrafish,ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14,Other,Through forward genetic screening for mutations affecting visual system development  we identified prominent coloboma and cell autonomous retinal neuron differentiation  lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present  most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp  which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when  and locations where  post mitotic cells have differentiated in wild type siblings. Indeed  RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated  for instance  in axon guidance  that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise  or promote transitions in  cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes.,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01,,,mutant1,SAMEA5059843,Department of Cell and Developmental Biology,ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059843|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant1|common name:zebrafish|sample name:ele mutant1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq 3000 paired end sequencing,ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:716 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP111778,Illumina HiSeq 3000 paired end sequencing,ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16,ele_A_CGATGT_L004_R1_001.fastq.gz ele_A_CGATGT_L004_R2_001.fastq.gz,fastq fastq,2181939600.0,10909698.0,ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 1,0:100 1:100,A:578028200;C:516249107;G:510965740;T:576417363;N:279190,100,100,,,578028200,516249107,510965740,576417363,279190,ERX2871394,ERS2871014,ERA1643817,Department of Cell and Developmental Biology|European Nucleotide Archive,Department of Cell and Developmental Biology,2,0.94968,0.94939,0.1131,0.11293,0.66245,0.66251,0.46654,0.47475,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2018-11-01,Undetermined,Embryo,Undetermined,Embryo Imprecise
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,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,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,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,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,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,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,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,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,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,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,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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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,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/β 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
10206,ERR6474244,ERX6101519,ERS7377049,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,InputFISH,E MTAB 10834:InputFISH,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:InputFISH p,InputFISH p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:input DNA|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,InputFISH.R1.fastq.gz InputFISH.R2.fastq.gz,fastq fastq,2014534500.0,24271500.0,E MTAB 10834:InputFISH.R,0:40 1:43,A:435725523;C:539145149;G:601092466;T:438298953;N:272409,40,43,,,435725523,539145149,601092466,438298953,272409,ERX6101519,ERS7377049,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.394,0.34957,0.09053,0.09378,0.96485,0.97323,0.73467,0.62676,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
10207,ERR6474223,ERX6101498,ERS7377028,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,hsHuRFISH rep2,E MTAB 10834:hsHuRFISH rep2,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:hsHuRFISH rep2 p,hsHuRFISH rep2 p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,hsHuRFISH_rep2.R2.fastq.gz hsHuRFISH_rep2.R1.fastq.gz,fastq fastq,2106598100.0,25380700.0,E MTAB 10834:hsHuRFISH rep2.R,0:40 1:43,A:503141361;C:548220448;G:569927989;T:485014455;N:293847,40,43,,,503141361,548220448,569927989,485014455,293847,ERX6101498,ERS7377028,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.76055,0.70626,0.18785,0.18742,0.92387,0.93533,0.72831,0.65481,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
10208,ERR6474222,ERX6101497,ERS7377027,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,hsHuRFISH rep1,E MTAB 10834:hsHuRFISH rep1,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:hsHuRFISH rep1 p,hsHuRFISH rep1 p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:anti hsHuR|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,hsHuRFISH_rep1.R1.fastq.gz hsHuRFISH_rep1.R2.fastq.gz,fastq fastq,2520623431.0,30368957.0,E MTAB 10834:hsHuRFISH rep1.R,0:40 1:43,A:604086659;C:653262791;G:679919989;T:582992802;N:361190,40,43,,,604086659,653262791,679919989,582992802,361190,ERX6101497,ERS7377027,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.76096,0.70783,0.18844,0.18848,0.92101,0.93275,0.7333,0.62616,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
10209,ERR6474221,ERX6101496,ERS7377026,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,HaloFISH,E MTAB 10834:HaloFISH,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:HaloFISH p,HaloFISH p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:anti HaloTag|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,HaloFISH.R2.fastq.gz HaloFISH.R1.fastq.gz,fastq fastq,2353027590.0,28349730.0,E MTAB 10834:HaloFISH.R,0:40 1:43,A:522964401;C:650152942;G:677020220;T:502555313;N:334714,40,43,,,522964401,650152942,677020220,502555313,334714,ERX6101496,ERS7377026,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.82307,0.78117,0.18309,0.18609,0.93888,0.94627,0.73861,0.63812,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
10210,ERR6474216,ERX6101492,ERS7377022,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,drHuRFISH rep2,E MTAB 10834:drHuRFISH rep2,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:drHuRFISH rep2 p,drHuRFISH rep2 p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,drHuRFISH_rep2.R1.fastq.gz drHuRFISH_rep2.R2.fastq.gz,fastq fastq,2408024386.0,29012342.0,E MTAB 10834:drHuRFISH rep2.R,0:40 1:43,A:566287649;C:627743498;G:663052609;T:550604982;N:335648,40,43,,,566287649,627743498,663052609,550604982,335648,ERX6101492,ERS7377022,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.68524,0.62721,0.16916,0.1656,0.93501,0.94541,0.7028,0.64738,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
10211,ERR6474215,ERX6101491,ERS7377021,ERP131171,PRJEB46937,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E-MTAB-10834,Other,RAP seq is a new method that provides in vitro derived RNA Interactomes for any given RBP. In RAP seq a recombinant RBP is produced as fusion with a HaloTag which is used to recover and purify the RBP of interest. The RBP Halo fusion is then incubated with fragmented total RNA derived from any given sample of interest. The bound RNA fragments are subsequently eluted and cloned using a small RNA library preparation protocol for sequencing the pool of bound molecules on an Illumina NGS platform.   In this study  RAP seq was used to identify RNA Interactomes of 26 novel RBPs aka non canonical RBPs newly discovered in proteome wide studies as RNA binders. RAP seq was also used to profile vertebrate HuR orthologs and described the biochemical evolutionary differences and similarities of the 6 orthologs profiled. Cancer associated IGF2BP1  IGF2BP2 and IGF2BP3 variants were also profiled and transcriptome wide changes in their RNA Interactomes with respect to the wild type IGF2BPs were reported. Also a transcriptome wide cooperative binding assay was perfomed to evaluate the cooperative roles of HuR and PTBP1 in binding to their native RNA targets.  In addition  a typical RAP seq substrate fragmented total RNA if reverse transcribed into cDNA and than in vitro transcribed again using a T7 RNA Polymerase can be depleted of any native endogenous RNA modifications and RAP seq assyas perfomed in parallel with the native substrate and the T7 RNAP produced one allowed us to discern the m6A dependency in transcriptome wide binding events for YTHDF1  hence with RAP seq we also report T7 RAP seq.,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,Protocols: HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,drHuRFISH rep1,E MTAB 10834:drHuRFISH rep1,,isolate:not applicable|disease:normal|ENA FIRST PUBLIC:2023 08 11T00:23:05Z|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 08 11T00:23:05Z|cell line:1|scientific name:Danio rerio|common name:zebrafish|organism part:liver|cell type:hepatocyte|genotype:wild type genotype|ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,,,,,,,,,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,E MTAB 10834:drHuRFISH rep1 p,drHuRFISH rep1 p,RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,HepG2 were obtained from American Type Culture Collection ATCC  Rockville  MD. The cell line was mycoplasma free when periodically tested with Mycoplasmacheck Eurofins Genomics. HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco's Modified Eagle Medium DMEM supplemented with 1/100 Penicillin/Streptomycin P/S  Sigma and 10 % fetal bovine serum Hyclone  GE healthcare. HepG2 cells were maintained by splitting 1/6 three times a week  done by aspirating the medium  gently washing the cells with phosphate buffered saline PBS  without xxx+  Sigma and detaching them with 2 mL of a trypsin EDTA solution 0.05%  Sigma for 3 5 min. Trypsin EDTA was inactivated with a minimum of 10 fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. post fragmentation  the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; post 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. three prime dephosphorylation was then performed with T4PNK in TAM buffer Tris Acetate 50 mM  Magnesium Chloride 10 mM  pH8.5 at room temperature for 4 hours followed by AMPure clean up and subsequently five prime phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions  then AMPure cleaned and aliquoted and stored at  80 degrees celsius until further used. Binding Assay: RBP Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit ThermoFisher and Wheat Germ extract according to manufacturers instructions 50 ul in vitro translation reaction. The in vitro translated proteins are recovered using 25 ul  Magne Halo Ligand beads Promega washed and resuspended in PBSN 1X PBS  0 005% NP 40 with added RNAse A and Turbo DNAse Thermo. post 1 hour of incubation  the beads are washed 4 times  twice with high salt PBSN + 1M MgCl2 and twice with normal salt PBSN. Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA 150 ng in total brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end over end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library.  Upon cell harvest  700 µL Qiazol QIAGEN was directly added onto the cells on ice and mixed. The cell extract was either stored at  80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min  before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely  and the pellet air dried for 5 minutes  before resuspension in nuclease free water. RNA concentration was determined by nanodrop Nanodrop 2000c. RNA was DNase treated using the Turbo DNase Kit Thermo Fisher for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit Zymo Research. The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3  PerkinElmer catalog # NOVA 5132 06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer's protocol.,Experimental Factor: immunoprecipitate:anti drHuR|Experimental Factor: organism:Danio rerio,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 550,,ERP131171,NextSeq 550 paired end sequencing; RNA Affinity Purification followed by sequencing RAP seq allows identification of transcriptome wide RBP binding sites using recombinant RBPs and total purified cellular RNA,ENA FIRST PUBLIC:2023 08 11|ENA LAST UPDATE:2023 08 11,drHuRFISH_rep1.R1.fastq.gz drHuRFISH_rep1.R2.fastq.gz,fastq fastq,3025188980.0,36448060.0,E MTAB 10834:drHuRFISH rep1.R,0:40 1:43,A:720153781;C:784188971;G:824077525;T:696330222;N:438481,40,43,,,720153781,784188971,824077525,696330222,438481,ERX6101491,ERS7377021,ERA5607540,"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive","Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden|European Nucleotide Archive",2,0.7001,0.64217,0.17626,0.1728,0.93154,0.94249,0.72494,0.65821,40,43,B,B,biological fallback assumption,illumina,nextseq,unknown,small_rna,unknown,bulk,unknown,unknown,,Sweden,2023-08-11,Undetermined,Undetermined,Multi-tissue,Multi-system
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,ERR7720665,ERX7289629,ERS9293395,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Nevi 3,SAMEA11646688,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646688|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Nevi 3 p,Nevi 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Nevi-3_1.fastq.gz Nevi-3_2.fastq.gz,fastq fastq,8483600160.0,53022501.0,E MTAB 7464 2:Nevi 3 ,0:80 1:80,A:2299114269;C:1922614492;G:1990271122;T:2270860686;N:739591,80,80,,,2299114269,1922614492,1990271122,2270860686,739591,ERX7289629,ERS9293395,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93346,0.93983,0.10878,0.10282,0.72608,0.72368,0.45081,0.44901,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10343,ERR7720664,ERX7289628,ERS9293394,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Nevi 2,SAMEA11646687,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646687|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Nevi 2 p,Nevi 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Nevi-2_1.fastq.gz Nevi-2_2.fastq.gz,fastq fastq,9002687680.0,56266798.0,E MTAB 7464 2:Nevi 2 ,0:80 1:80,A:2446965759;C:2045918133;G:2107744175;T:2400665463;N:1394150,80,80,,,2446965759,2045918133,2107744175,2400665463,1394150,ERX7289628,ERS9293394,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93879,0.94198,0.1057,0.10023,0.7289,0.72874,0.45656,0.45677,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10344,ERR7720663,ERX7289627,ERS9293393,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Nevi 1,SAMEA11646686,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646686|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Nevi 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanocytic nevus|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Nevi 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Nevi 1 p,Nevi 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanocytic nevus,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Nevi-1_1.fastq.gz Nevi-1_2.fastq.gz,fastq fastq,9332077600.0,58325485.0,E MTAB 7464 2:Nevi 1 ,0:80 1:80,A:2559136296;C:2096458598;G:2152359634;T:2522670596;N:1452476,80,80,,,2559136296,2096458598,2152359634,2522670596,1452476,ERX7289627,ERS9293393,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93341,0.93788,0.12721,0.12045,0.71181,0.71104,0.45834,0.46252,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10345,ERR7720662,ERX7289626,ERS9293392,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Melanoma 4,SAMEA11646685,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646685|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 4|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Melanoma 4 p,Melanoma 4 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Melanoma-4_1.fastq.gz Melanoma-4_2.fastq.gz,fastq fastq,8435873280.0,52724208.0,E MTAB 7464 2:Melanoma 4 ,0:80 1:80,A:2339229980;C:1858003608;G:1925352938;T:2311974102;N:1312652,80,80,,,2339229980,1858003608,1925352938,2311974102,1312652,ERX7289626,ERS9293392,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93101,0.93509,0.11646,0.10875,0.73647,0.73742,0.5229,0.52491,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10346,ERR7720661,ERX7289625,ERS9293391,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Melanoma 3,SAMEA11646684,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646684|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Melanoma 3 p,Melanoma 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Melanoma-3_1.fastq.gz Melanoma-3_2.fastq.gz,fastq fastq,8652678880.0,54079243.0,E MTAB 7464 2:Melanoma 3 ,0:80 1:80,A:2358154757;C:1941914032;G:2017842865;T:2333420807;N:1346419,80,80,,,2358154757,1941914032,2017842865,2333420807,1346419,ERX7289625,ERS9293391,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93095,0.93482,0.11494,0.10979,0.74878,0.74801,0.54149,0.54333,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10347,ERR7720660,ERX7289624,ERS9293390,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Melanoma 2,SAMEA11646683,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646683|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Melanoma 2 p,Melanoma 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Melanoma-2_1.fastq.gz Melanoma-2_2.fastq.gz,fastq fastq,9474565280.0,59216033.0,E MTAB 7464 2:Melanoma 2 ,0:80 1:80,A:2592490883;C:2143181332;G:2197827206;T:2539575741;N:1490118,80,80,,,2592490883,2143181332,2197827206,2539575741,1490118,ERX7289624,ERS9293390,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93925,0.94448,0.10906,0.10386,0.73768,0.73722,0.51879,0.51954,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10348,ERR7720659,ERX7289623,ERS9293389,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Melanoma 1,SAMEA11646682,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646682|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Melanoma 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:melanoma|genotype:kita GFP RAS|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Melanoma 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Melanoma 1 p,Melanoma 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:kita GFP RAS|Experimental Factor: injury:n1|Experimental Factor: disease:melanoma,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Melanoma-1_1.fastq.gz Melanoma-1_2.fastq.gz,fastq fastq,8202724480.0,51267028.0,E MTAB 7464 2:Melanoma 1 ,0:80 1:80,A:2226523748;C:1862763739;G:1929197629;T:2182962113;N:1277251,80,80,,,2226523748,1862763739,1929197629,2182962113,1277251,ERX7289623,ERS9293389,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93514,0.9398,0.10447,0.09961,0.71697,0.71715,0.50157,0.50305,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10349,ERR7720658,ERX7289622,ERS9293388,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl R 4,SAMEA11646681,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646681|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 4|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 4|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl R 4 p,Ctrl R 4 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-R-4_1.fastq.gz Ctrl-R-4_2.fastq.gz,fastq fastq,12134105440.0,75838159.0,E MTAB 7464 2:Ctrl R 4 ,0:80 1:80,A:3262023701;C:2677095735;G:2964643096;T:3227367048;N:2975860,80,80,,,3262023701,2677095735,2964643096,3227367048,2975860,ERX7289622,ERS9293388,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.91148,0.90942,0.31684,0.30692,0.7517,0.75708,0.51896,0.51898,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10350,ERR7720657,ERX7289621,ERS9293387,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl R 3,SAMEA11646680,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646680|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl R 3 p,Ctrl R 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-R-3_1.fastq.gz Ctrl-R-3_2.fastq.gz,fastq fastq,10198941920.0,63743387.0,E MTAB 7464 2:Ctrl R 3 ,0:80 1:80,A:2707258482;C:2295053882;G:2521099885;T:2673029444;N:2500227,80,80,,,2707258482,2295053882,2521099885,2673029444,2500227,ERX7289621,ERS9293387,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.88031,0.87949,0.30603,0.30519,0.76219,0.76798,0.52516,0.51963,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10351,ERR7720656,ERX7289620,ERS9293386,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl R 2,SAMEA11646679,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646679|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl R 2 p,Ctrl R 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-R-2_1.fastq.gz Ctrl-R-2_2.fastq.gz,fastq fastq,13001272960.0,81257956.0,E MTAB 7464 2:Ctrl R 2 ,0:80 1:80,A:3429977204;C:2902807573;G:3288394622;T:3376870832;N:3222729,80,80,,,3429977204,2902807573,3288394622,3376870832,3222729,ERX7289620,ERS9293386,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.89444,0.89377,0.30516,0.30529,0.75773,0.76769,0.52784,0.52192,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10352,ERR7720655,ERX7289619,ERS9293385,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl R 1,SAMEA11646678,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646678|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl R 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl R 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl R 1 p,Ctrl R 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-R-1_1.fastq.gz Ctrl-R-1_2.fastq.gz,fastq fastq,10689399040.0,66808744.0,E MTAB 7464 2:Ctrl R 1 ,0:80 1:80,A:2897858681;C:2320332197;G:2613694217;T:2854881563;N:2632382,80,80,,,2897858681,2320332197,2613694217,2854881563,2632382,ERX7289619,ERS9293385,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.87124,0.87083,0.30804,0.30796,0.74596,0.75668,0.49784,0.50675,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10353,ERR7720654,ERX7289618,ERS9293384,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl MN 3,SAMEA11646677,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646677|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl MN 3 p,Ctrl MN 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-MN-3_1.fastq.gz Ctrl-MN-3_2.fastq.gz,fastq fastq,7551734240.0,47198339.0,E MTAB 7464 2:Ctrl MN 3 ,0:80 1:80,A:2046757744;C:1713576176;G:1763123655;T:2027090307;N:1186358,80,80,,,2046757744,1713576176,1763123655,2027090307,1186358,ERX7289618,ERS9293384,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93513,0.93893,0.11198,0.10677,0.7232,0.72267,0.44068,0.4478,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10354,ERR7720653,ERX7289617,ERS9293383,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl MN 2,SAMEA11646676,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646676|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl MN 2 p,Ctrl MN 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-MN-2_1.fastq.gz Ctrl-MN-2_2.fastq.gz,fastq fastq,8217322560.0,51358266.0,E MTAB 7464 2:Ctrl MN 2 ,0:80 1:80,A:2206636607;C:1895861057;G:1945883692;T:2167661877;N:1279327,80,80,,,2206636607,1895861057,1945883692,2167661877,1279327,ERX7289617,ERS9293383,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.94029,0.94525,0.10143,0.09713,0.72251,0.72036,0.44465,0.44591,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10355,ERR7720652,ERX7289616,ERS9293382,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Ctrl MN 1,SAMEA11646675,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646675|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:Ctrl MN 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:mitfa+/ |injury:n1|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:Ctrl MN 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:Ctrl MN 1 p,Ctrl MN 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:n1|Experimental Factor: genotype:mitfa+/ |Experimental Factor: injury:n1|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,Ctrl-MN-1_1.fastq.gz Ctrl-MN-1_2.fastq.gz,fastq fastq,8135337280.0,50845858.0,E MTAB 7464 2:Ctrl MN 1 ,0:80 1:80,A:2202274973;C:1853973619;G:1910166269;T:2167658174;N:1264245,80,80,,,2202274973,1853973619,1910166269,2167658174,1264245,ERX7289616,ERS9293382,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.93729,0.94287,0.10448,0.09933,0.72585,0.72612,0.45373,0.45518,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10356,ERR7720651,ERX7289615,ERS9293381,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,7dpa 3,SAMEA11646674,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646674|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:7dpa 3 p,7dpa 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,7dpa-3_1.fastq.gz 7dpa-3_2.fastq.gz,fastq fastq,9873881440.0,61711759.0,E MTAB 7464 2:7dpa 3 ,0:80 1:80,A:2682240945;C:2177286149;G:2380282226;T:2631847017;N:2225103,80,80,,,2682240945,2177286149,2380282226,2631847017,2225103,ERX7289615,ERS9293381,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.83718,0.84277,0.3425,0.34639,0.73801,0.75035,0.51021,0.49835,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10357,ERR7720650,ERX7289614,ERS9293380,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,7dpa 2,SAMEA11646673,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646673|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:7dpa 2 p,7dpa 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,7dpa-2_1.fastq.gz 7dpa-2_2.fastq.gz,fastq fastq,12193073280.0,76206708.0,E MTAB 7464 2:7dpa 2 ,0:80 1:80,A:3333326821;C:2692186511;G:2887657057;T:3277111703;N:2791188,80,80,,,3333326821,2692186511,2887657057,3277111703,2791188,ERX7289614,ERS9293380,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.84944,0.85085,0.36391,0.36512,0.72496,0.73511,0.50367,0.49643,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10358,ERR7720649,ERX7289613,ERS9293379,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,7dpa 1,SAMEA11646672,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646672|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:7dpa 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:7dpa 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:7dpa 1 p,7dpa 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,7dpa-1_1.fastq.gz 7dpa-1_2.fastq.gz,fastq fastq,11533139040.0,72082119.0,E MTAB 7464 2:7dpa 1 ,0:80 1:80,A:3069170319;C:2575356466;G:2889466424;T:2996503729;N:2642102,80,80,,,3069170319,2575356466,2889466424,2996503729,2642102,ERX7289613,ERS9293379,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.86542,0.86857,0.33902,0.34263,0.7288,0.74186,0.50529,0.50071,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10359,ERR7720648,ERX7289612,ERS9293378,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,1dpa 3,SAMEA11646671,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646671|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 3|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 3|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:1dpa 3 p,1dpa 3 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,1dpa-3_1.fastq.gz 1dpa-3_2.fastq.gz,fastq fastq,13728291840.0,85801824.0,E MTAB 7464 2:1dpa 3 ,0:80 1:80,A:3747242594;C:3041779368;G:3248651209;T:3687437813;N:3180856,80,80,,,3747242594,3041779368,3248651209,3687437813,3180856,ERX7289612,ERS9293378,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.90779,0.9111,0.34976,0.34957,0.72827,0.73499,0.50071,0.49578,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10360,ERR7720647,ERX7289611,ERS9293377,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,1dpa 2,SAMEA11646670,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646670|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 2|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 2|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:1dpa 2 p,1dpa 2 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,1dpa-2_1.fastq.gz 1dpa-2_2.fastq.gz,fastq fastq,12524780320.0,78279877.0,E MTAB 7464 2:1dpa 2 ,0:80 1:80,A:3452368285;C:2754592593;G:2905324477;T:3409605329;N:2889636,80,80,,,3452368285,2754592593,2905324477,3409605329,2889636,ERX7289611,ERS9293377,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.90773,0.91019,0.32749,0.32608,0.73756,0.74172,0.51153,0.50818,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
10361,ERR7720646,ERX7289610,ERS9293376,ERP133910,PRJEB49404,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E-MTAB-7464_2,Transcriptome Analysis,Zebrafish have the ability to regenerate many organs and tissues including the melanocytes which are elements of the skin. RNA sequencing RNA Seq is a high throughput sequencing method facilitating transcript identification and quantification of gene expression in a precise manner. The development of RNA Seq technologies and their extensive data analysis methods make an investigation of regulatory genes and functional gene annotations possible under specific conditions. Here  we aim to perform large scale comparative deep transcriptome profiling of regeneration versus cancer in the following two cellular contexts: The skin melanocytes  which can substantially regenerate in mammals and melanoma which is the type of cancer that begins in the melanocytes.,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,,Protocols: Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin. Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Center's Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC. The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 µM NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation. RNA isolation was carried out according to the manufacturer's instructions on the procedure “Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent” in RNeasy® Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,1dpa 1,SAMEA11646669,Izmir Biomedicine and Genome Center / Turkey,ENA FIRST PUBLIC:2022 12 29|ENA LAST UPDATE:2022 12 29|External Id:SAMEA11646669|INSDC center alias:Izmir Biomedicine and Genome Center / Turkey|INSDC center name:Izmir Biomedicine and Genome Center / Turkey|INSDC first public:2022 12 29T00:21:02Z|INSDC last update:2022 12 29T00:21:02Z|INSDC status:public|Submitter Id:E MTAB 7464 2:1dpa 1|age:6 to 10|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|injury:melanocyte ablation|isolate:not applicable|organism part:caudal fin|sample name:E MTAB 7464 2:1dpa 1|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,E MTAB 7464 2:1dpa 1 p,1dpa 1 p,Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,Following NCP treatment  caudal fins of individuals were collected for each group control  1 dpa  7 dpa  nevi and melanoma and used as biological replicates not pooled. Zebrafish melanoma model was generated by breeding Tgmitfa / ; kita:GFP RASG12V line with wild type strain AB. Siblings of the breeds mitfa+/  were used as non tumorigenic control groups. The ages of the fish ranged between 6 month 12 month. First  fish were anesthetized by Tricaine 10 mg/mL MilliporeSigma  A5040 25G  then  once fish were immobilized  the caudal fin of each fish was resected with a razor blade. Four animals were used for each stage. The dorsoventral resection was performed at half of the caudal fin to obtain maximum content without xxx the regeneration potential of the fin.  Zebrafish are maintained in accordance with the guidelines of the Izmir Biomedicine and Genome Centers Animal Care and Use Committee. All animal experiments were performed with the approval of the Animal Experiments Local Ethics Committee of Izmir Biomedicine and Genome Center IBG AELEC.  The zebrafish melanocyte regeneration model in this study was generated by using Neocuproine NCP  which specifically kills mature melanocytes without xxx harm to mitf+ melanocyte progenitor cells. Adult zebrafish of 6 month 12 month of age were subjected to 1 M NCP for 24 hours and then caudal fin tissue samples were collected at the days of 1 dpa and 7 dpa days post ablation.  RNA isolation was carried out according to the manufacturer's instructions on the procedure Appendix C: RNA Cleanup post Lysis and Homogenization with QIAzol Lysis Reagent in RNeasy Micro Handbook. Fins were immersed into QIAzol Lysis Reagent then immediately proceeded to tissue disruption and homogenization.  RNA seq libraries were built using the TruSeq RNA Library Preparation Kit from Illumina,Experimental Factor: compound:neocuproine|Experimental Factor: dose:1|Experimental Factor: genotype:wild type genotype|Experimental Factor: injury:melanocyte ablation|Experimental Factor: disease:normal,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,ERP133910,NextSeq 500 paired end sequencing; Comparative analysis of the molecular mechanisms of melanocyte regeneration and melanoma using the zebrafish model,ENA FIRST PUBLIC:2023 01 03|ENA LAST UPDATE:2023 01 03,1dpa-1_1.fastq.gz 1dpa-1_2.fastq.gz,fastq fastq,15395445120.0,96221532.0,E MTAB 7464 2:1dpa 1 ,0:80 1:80,A:4187891415;C:3447519966;G:3632085998;T:4124408897;N:3538844,80,80,,,4187891415,3447519966,3632085998,4124408897,3538844,ERX7289610,ERS9293376,ERA7895107,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,Izmir Biomedicine and Genome Center / Turkey|European Nucleotide Archive,2,0.90197,0.907,0.33556,0.33653,0.73724,0.74546,0.51071,0.50585,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,Turkey,2022-12-29,Adult,Adult,Multi-tissue,Multi-system
25182,SRR25670729,SRX21396042,SRS18636200,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA germ ring PAL seq v4,GSM7716871,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA germ ring PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716871,GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER,GSM7716871 r1,GSM7716871,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read2.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep1_raw_read1.fastq.gz,fastq fastq,2834842912.0,9234016.0,GSM7716871 r1,0:52 1:255,A:725811118;C:702410592;G:747583409;T:651018348;N:8019445,52,255,,,725811118,702410592,747583409,651018348,8019445,SRX21396042,SRS18636200,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00023,0.30494,8e-05,0.01793,0.99967,0.99971,0.5,1.0,52,255,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25183,SRR25670730,SRX21396042,SRS18636200,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA germ ring PAL seq v4,GSM7716871,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA germ ring PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716871,GSM7716871: Fish embryo mRNA germ ring PAL seq v4; Danio rerio; OTHER,GSM7716871 r1,GSM7716871,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_germ_ring_PAL_seq_v4_rep2_raw_read2.fastq.gz,fastq fastq,3473033898.0,11312814.0,GSM7716871 r2,0:52 1:255,A:853178471;C:899976159;G:962100712;T:750811461;N:6967095,52,255,,,853178471,899976159,962100712,750811461,6967095,SRX21396042,SRS18636200,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00049,0.0,0.00012,0.0,0.99941,1.0,0.64864,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25184,SRR25670731,SRX21396041,SRS18636199,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA zfs:0000015 PAL seq v4,GSM7716870,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA zfs:0000015 PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716870,GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER,GSM7716870 r1,GSM7716870,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep1_raw_read2.fastq.gz,fastq fastq,2695203962.0,8779166.0,GSM7716870 r1,0:52 1:255,A:684535386;C:669852151;G:719008886;T:614209811;N:7597728,52,255,,,684535386,669852151,719008886,614209811,7597728,SRX21396041,SRS18636199,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00117,0.35837,0.00017,0.00682,0.99859,0.99963,0.69473,1.0,52,255,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25185,SRR25670732,SRX21396041,SRS18636199,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA zfs:0000015 PAL seq v4,GSM7716870,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA zfs:0000015 PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716870,GSM7716870: Fish embryo mRNA zfs:0000015 PAL seq v4; Danio rerio; OTHER,GSM7716870 r1,GSM7716870,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read2.fastq.gz Fish_embryo_mRNA_30percent_epiboly_PAL_seq_v4_rep2_raw_read1.fastq.gz,fastq fastq,3476338446.0,11323578.0,GSM7716870 r2,0:52 1:255,A:841832234;C:898325199;G:968774318;T:760398070;N:7008625,52,255,,,841832234,898325199,968774318,760398070,7008625,SRX21396041,SRS18636199,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00245,0.0,0.00047,0.0,0.99803,1.0,0.58536,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25186,SRR25670733,SRX21396040,SRS18636198,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA sphere PAL seq v4,GSM7716869,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA sphere PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716869,GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER,GSM7716869 r1,GSM7716869,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep1_raw_read2.fastq.gz,fastq fastq,3211687254.0,10461522.0,GSM7716869 r1,0:52 1:255,A:813560400;C:775326762;G:854563477;T:759161458;N:9075157,52,255,,,813560400,775326762,854563477,759161458,9075157,SRX21396040,SRS18636198,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00088,0.43191,0.0004,0.01556,0.99916,0.99961,0.55769,1.0,52,255,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25187,SRR25670734,SRX21396040,SRS18636198,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA sphere PAL seq v4,GSM7716869,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA sphere PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716869,GSM7716869: Fish embryo mRNA sphere PAL seq v4; Danio rerio; OTHER,GSM7716869 r1,GSM7716869,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read1.fastq.gz Fish_embryo_mRNA_sphere_PAL_seq_v4_rep2_raw_read2.fastq.gz,fastq fastq,3179916131.0,10358033.0,GSM7716869 r2,0:52 1:255,A:771755667;C:804256300;G:883166175;T:714242073;N:6495916,52,255,,,771755667,804256300,883166175,714242073,6495916,SRX21396040,SRS18636198,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.00186,0.0,0.00088,0.0,0.99862,1.0,0.64705,,52,255,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
25188,SRR25670735,SRX21396039,SRS18636197,SRP455680,PRJNA1006406,Control of polyA tail length and translation in vertebrate oocytes and early embryos,GSE241107,Other,During oocyte maturation and early embryonic development  polyA tail lengths strongly influence mRNA translation. However  how tail lengths are controlled at different developmental stages has been unclear. Here  we performed tail length and translational profiling of mRNA reporter libraries each with > 10 million three prime UTR sequence variants in frog oocytes and embryos  and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5 mer. Additional sequence motifs drive stage specific deadenylation in embryos  and UUUUA and C rich motifs drive tail length independent translational repression in oocytes. A neural network model accurately predicts tail length change during oocyte maturation in frogs  mice  and humans. Analyses of human sequence variants showed that those predicted to disrupt tail length control have been under negative selection  implying that our insights into control of polyA tail length and translation have implications for human health and fertility. Overall design: Sythetic mRNA reporter libraries with random three prime UTR sequences under four different sequence contexts were injected into frog oocytes and embryos and fish embryos. PolyA tail lengths were measured to at different developmental stages to examine sequence motifs that caused tail length changes. At the same time  polyA tail lengths of endogenous mRNAs from frog oocytes and embryos  fish embryos  and mouse oocytes were measured to investiage how their tail lengths were controlled. Please note that sample titles have been updated on Jan 6  2024.,,,,Fish embryo mRNA 1024cell PAL seq v4,GSM7716868,,source name:embryo|tissue:embryo|treatment:N1|geo loc name:missing|collection date:missing,Fish embryo mRNA 1024cell PAL seq v4,For gene specific tail seq of mRNA reporters  data were processed with a custom script available at https://github.com/coffeebond/MPRA tail seq. For PAL seq v3 or v4  reads were trimmed with cutadapt v3.7 with the parameters “ m 15   quality base=64  q 20 20   match read wildcards  e 0.05  a NNNNATCTCGTATGCCGTCTTCTGCTTG  O 7”. The trimmed reads were mapped using STAR v2.7.1a to the reference database containing the genomic sequences of the organism from which the mRNAs were obtained  the genomic sequences of humans or fish  depending on which spike in RNAs were used  and the sequences of the polyA standards generated previously  with the parameters “  runThreadN 16   runMode alignReads   outFilterMultimapNmax 1   outReadsUnmapped Fastx   outFilterType BySJout   outSAMattributes All   outSAMtype BAM Unsorted SortedByCoordinate”. Uniquely mapped read were furhter processed with a custom script available at https://github.com/coffeebond/PAL seq. Assembly: Homo sapiens: GRCh38.p7 primary assembly. Mus muculus: GRCh38.p4  primary assembly. Xenopus laevis: v10.1 assembly. Danio rerio: GRCz11 assembly. Supplementary files format and content: For gene specific tail seq of mRNA reporters  tab delimited text files with columns indicating 1 sequence of the variable region; 2 median tail length; 3 number of reads; 4–7 tail lengths at quantile 10  25  75  and 90. Supplementary files format and content: For PAL seq v3 or v4  tab delimited files with columns indicating 1 gene ID or polyA site ID; 2 read cluster ID; 3 tail length Library strategy: PAL seq v4,embryo,,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer’s suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,tissue:embryo|treatment:N1,GSM7716868,GSM7716868: Fish embryo mRNA 1024cell PAL seq v4; Danio rerio; OTHER,GSM7716868 r1,GSM7716868,1,Frog oocytes and embryos were lysed in ice cold buffer RL 20 mM HEPES pH 7.5  100 mM KCl  5 mM MgCl2  1% [v/v] Triton X 100  100 µg/ml cycloheximide  cOmplete protease inhibitor cocktail [1 tablet per 10 ml buffer]  and 200 units/ml SUPERase•In in a volume of 10 µl per oocyte/embryo by vigorous shaking and pipetting. Lysates were cleared by centrifugation at 5000 g at 4°C for 10 min. The supernatant was transfered to a new tube and mixed with the Tri reagent for RNA isolation. Fish embryos were de chorionated by incubation with 2 mg/ml pronase in E3 medium for 4 min. post removing all E3 medium  Tri Reagent was added to the embryos for RNA isolation. Mouse GV oocytes were collected in 37°C MEM in the presence of milrinone to prevent maturation. Cumulus cells were removed from cumulus oocyte complexes by repeated aspiration through a glass pipette. GV oocytes were then collected in TRI reagent for RNA isolation. Mouse MII oocytes were harvested from the oviducts of hCG induced mice 16 hr  denuded with 3 mg/ml hyaluronidase for 2 min  washed  and then collected in Tri reagent for RNA isolation. For gene specific tail seq of reporter libraries  total RNA with reporter mRNA libraries was ligated to a pre adenylated 3ʹ adapter directly in most cases  but for the N60 library injected into fish embryos and frog oocytes  the N37 PAS N17 library injected into fish embryos and frog oocytes  and the CPEmos N60 and N60LC PASmos libraries injected into frog oocytes  reporter library mRNAs were enriched by anti sense oligo capture with biotinylated oligos. RNA isolated from the oocyte or embryo lysate was mixed with 8 pmol KXSH009  8 pmol KXSH010  and 2x SSC 0.3 M NaCl  30 mM sodium citrate pH 7.0 in a total of 50 µl. The RNA and oligos were annealed by incubation at 70°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 40 µl MyOne Streptavidin C1 beads Thermo Fisher  65002 and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack and removed. The beads were washed twice with 300 µl 1xB&W buffer 5 mM Tris HCl pH 7.5  0.5 mM EDTA  1 M NaCl and once with 300 µl 2x SSC. The RNA was eluted from the beads first with 100 µl 10 mM HEPES pH 7.5 at 65°C for 3 min and then second with 100 µl water at 65°C for 3 min. The eluates were combined  precipitated with ethanol  and resuspended in 6.5 µl water. The anti sense oligo enriched RNA or the RNA isolated from oocyte or embryo lysates was ligated to a pre adenylated 3ʹ adapter in a 10 µl reaction containing 5 µM 3ʹ adapter KXS330  50 mM HEPES pH 7.5  10 mM MgCl2  10 mM dithiothreitol  1 unit/µl T4 RNA ligase 1 New England Biolabs  M0204S. The ligation reaction was incubated at 23°C for 150 min. post ligation  RNA was extracted with phenol/chloroform  precipitated with ethanol  and resuspended in 11.4 µl water. The ligated RNA was mixed with 0.6 µl 100 µM reverse transcription primer KXS037 in a total volume of 12 µl  incubated at 65°C for 5 min  and cooled on ice for 1 min. The annealed RNA was reverse transcribed in a 20 µl reaction containing 1x First Strand Buffer  500 µM dNTPs  5 mM dithiothreitol  1 unit/µl SUPERase•In  and 200 units SuperScript III Thermo Fisher  18080044 at 50°C for 1 hr. post reverse transcription  RNA was hydrolyzed with 3.3 µl 1 M NaOH at 90°C for 10 min  followed by neutralization with 36.7 µl 1 M HEPES pH 7.5 and the cDNA was collected by desalting with a Micro Bio Spin P 30 column. The cDNA library was amplified in a 50 µl PCR reaction with KXS037 and a barcoded primer Supplemental using the KAPA HiFi HotStart Kits following the manufacturer's suggested protocol for 10–15 cycles. The PCR amplified library was cleaned up twice with AMPure XP beads Beckman Coulter  A63881 with a beads to sample ratio of 1.2. For sequencing of endogenous mRNA polyA tail length  libraries were prepared with PAL seq v3 for frog oocytes or PAL seq v4 for frog embryos  fish embryos  and mouse oocytes as described previously PMID: 34213414. When preparing the sequencing libraries of mRNAs from fish embryos  a different 3ʹ adapter KXS013 was used for 3ʹ end ligation  and polyA selected mRNA from HeLa cells was used as spike in  replacing polyA selected mRNA from zebrafish ZF4 cell line. The first round of sequencing results suggested that a large fraction of the fish mRNA libraries was 5.8S rRNA. The cDNA of 5.8S rRNA was depleted from the cDNA libraries with an antisense oligo. The seven cDNA libraries made from mRNAs of zebrafish embryos at different stages were mixed at roughly equal molar ratios in a total of 5 fmol. Fifty pmol KXSH015 and 2x SSC were added in a total of 100 µl. The cDNAs and the oligo were annealed by incubation at 65°C for 5 min and then slowly cooling to 23°C at 0.1°C/sec. The annealed mixture was combined with 100 µl MyOne Streptavidin C1 beads and incubated for 20 min at 23°C on a thermal mixer  shaking with 15 sec on and 1 min 45 sec off. The supernatant was separated from the beads with a magnetic rack. The beads were washed once with 200 µl 1xB&W buffer. The supernatant and the wash were combined  precipitated with ethanol  and resuspended in 30 µl water. The oligo depleted libraries were sequenced again as a technical replicate. Sequencing data of replicates were merged for each sample post monitoring consistency.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP455680,,,Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read1.fastq.gz Fish_embryo_mRNA_1024cell_PAL_seq_v4_rep1_raw_read2.fastq.gz,fastq fastq,2191900794.0,7139742.0,GSM7716868 r1,0:52 1:255,A:571954354;C:551162617;G:572445400;T:490238669;N:6099754,52,255,,,571954354,551162617,572445400,490238669,6099754,SRX21396039,SRS18636197,SRA1694849,Whitehead Institute,Whitehead Institute,2,0.0011,0.43387,6e-05,0.01058,0.99864,0.99971,0.74576,1.0,52,255,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2023-08-17,Zygote,Embryo,Embryo Imprecise,All anatomical structures