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
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
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
28725,SRR26623262,SRX22323921,SRS19374450,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  cirbpb scars,GSM7875190,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  cirbpb scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875190,GSM7875190: Lineage tracing rep1  cirbpb scars; Danio rerio; OTHER,GSM7875190 r1,GSM7875190,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz,fastq fastq,157576336.0,949552.0,GSM7875190 r1,,,,,,,,,,,,SRX22323921,SRS19374450,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00141,0.78069,0.00053,0.00877,0.99857,0.97822,0.33536,0.05199,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28726,SRR26623263,SRX22323920,SRS19374449,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  cfl1 scars,GSM7875189,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  cfl1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875189,GSM7875189: Lineage tracing rep1  cfl1 scars; Danio rerio; OTHER,GSM7875189 r1,GSM7875189,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz,fastq fastq,381453696.0,2184402.0,GSM7875189 r1,,,,,,,,,,,,SRX22323920,SRS19374449,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.0002,0.91626,0.00014,0.00132,0.99987,0.99726,0.16666,0.56363,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28727,SRR26623264,SRX22323919,SRS19374448,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  actb2 scars,GSM7875188,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  actb2 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875188,GSM7875188: Lineage tracing rep1  actb2 scars; Danio rerio; OTHER,GSM7875188 r1,GSM7875188,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz,fastq fastq,491682118.0,2851156.0,GSM7875188 r1,,,,,,,,,,,,SRX22323919,SRS19374448,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00051,0.41901,0.00032,0.0029,0.99945,0.99182,0.57575,0.007,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28728,SRR26623265,SRX22323918,SRS19374446,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  actb1 scars,GSM7875187,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  actb1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875187,GSM7875187: Lineage tracing rep1  actb1 scars; Danio rerio; OTHER,GSM7875187 r1,GSM7875187,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz,fastq fastq,390405832.0,2283319.0,GSM7875187 r1,,,,,,,,,,,,SRX22323918,SRS19374446,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00038,0.73548,0.00017,0.00057,0.99963,0.99571,0.29729,0.00243,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28729,SRR26623266,SRX22323917,SRS19374447,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Brain 23   telencephalon  Notch inhibition  scSLAMseq,GSM7875186,,source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT|geo loc name:missing|collection date:missing,Brain 23   telencephalon  Notch inhibition  scSLAMseq,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq,adult brain,Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT Gamma Secretase Inhibitor  Sigma Aldrich for 48 hours.,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT,GSM7875186,GSM7875186: Brain 23   telencephalon  Notch inhibition  scSLAMseq; Danio rerio; OTHER,GSM7875186 r1,GSM7875186,1,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz,fastq fastq,62392458570.0,271271559.0,GSM7875186 r1,0:28 1:202,A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393,28,202,,,18682905645,13783082970,14751373116,15161083446,14013393,SRX22323917,SRS19374447,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.01404,0.82351,0.00466,0.1026,0.99129,0.86774,0.36033,0.67345,28,202,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28730,SRR26623267,SRX22323916,SRS19374445,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Brain 22   telencephalon  control  scSLAMseq,GSM7875185,,source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO|geo loc name:missing|collection date:missing,Brain 22   telencephalon  control  scSLAMseq,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq,adult brain,Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO,GSM7875185,GSM7875185: Brain 22   telencephalon  control  scSLAMseq; Danio rerio; OTHER,GSM7875185 r1,GSM7875185,1,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz,fastq fastq,59793114490.0,259970063.0,GSM7875185 r1,0:28 1:202,A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613,28,202,,,18600519530,12714987967,14147370465,14316863915,13372613,SRX22323916,SRS19374445,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.01402,0.79448,0.00498,0.11405,0.99074,0.8518,0.39874,0.67082,28,202,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28754,SRR26623291,SRX22323897,SRS19374426,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  ube2e1 scars,GSM7875196,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  ube2e1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875196,GSM7875196: Lineage tracing rep2  ube2e1 scars; Danio rerio; OTHER,GSM7875196 r1,GSM7875196,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz,fastq fastq,213092161.0,1190459.0,GSM7875196 r1,,,,,,,,,,,,SRX22323897,SRS19374426,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00752,0.90776,0.00286,0.01739,0.99346,0.95444,0.46002,0.96817,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28755,SRR26623292,SRX22323896,SRS19374425,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  rpl39 scars,GSM7875195,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  rpl39 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875195,GSM7875195: Lineage tracing rep2  rpl39 scars; Danio rerio; OTHER,GSM7875195 r1,GSM7875195,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz,fastq fastq,1023403502.0,5717338.0,GSM7875195 r1,,,,,,,,,,,,SRX22323896,SRS19374425,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00086,0.83744,0.0003,0.00337,0.99845,0.97057,0.26605,0.40241,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28756,SRR26623293,SRX22323895,SRS19374424,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  cirbpb scars,GSM7875194,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  cirbpb scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875194,GSM7875194: Lineage tracing rep2  cirbpb scars; Danio rerio; OTHER,GSM7875194 r1,GSM7875194,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz,fastq fastq,276120388.0,1542572.0,GSM7875194 r1,,,,,,,,,,,,SRX22323895,SRS19374424,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00206,0.80328,0.00078,0.00662,0.9975,0.98039,0.55421,0.0258,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28757,SRR26623294,SRX22323894,SRS19374423,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  cfl1 scars,GSM7875193,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  cfl1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875193,GSM7875193: Lineage tracing rep2  cfl1 scars; Danio rerio; OTHER,GSM7875193 r1,GSM7875193,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz,fastq fastq,791318009.0,4420771.0,GSM7875193 r1,,,,,,,,,,,,SRX22323894,SRS19374423,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00067,0.46079,0.00055,0.16353,0.99965,0.99332,0.52631,0.44939,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28758,SRR26623295,SRX22323893,SRS19374421,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  ube2e1 scars,GSM7875192,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  ube2e1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875192,GSM7875192: Lineage tracing rep1  ube2e1 scars; Danio rerio; OTHER,GSM7875192 r1,GSM7875192,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz,fastq fastq,99407618.0,601781.0,GSM7875192 r1,,,,,,,,,,,,SRX22323893,SRS19374421,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00657,0.84532,0.00205,0.03049,0.99537,0.95286,0.43306,0.19203,28,150,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28759,SRR26623296,SRX22323892,SRS19374422,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  rpl39 scars,GSM7875191,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  rpl39 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875191,GSM7875191: Lineage tracing rep1  rpl39 scars; Danio rerio; OTHER,GSM7875191 r1,GSM7875191,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz,fastq fastq,401898718.0,2276836.0,GSM7875191 r1,,,,,,,,,,,,SRX22323892,SRS19374422,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00037,0.2642,0.00015,0.00086,0.99922,0.99026,0.23076,0.42455,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
43990,SRR6811825,SRX3768865,SRS3023383,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 3 scar,GSM3032168,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 3 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM3032168,GSM3032168: Brain 3 scar; Danio rerio; OTHER,GSM3032168,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032168,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,B7_scar_R2.fastq.gz B7_scar_R1.fastq.gz,fastq fastq,1359725968.0,10965532.0,GSM3032168 r1,0:26 1:98,A:397239266;C:429529094;G:288126336;T:244165622;N:665650,26,98,,,397239266,429529094,288126336,244165622,665650,SRX3768865,SRS3023383,SRA623333,GEO,Max Delbrück Center,2,0.00032,0.00295,0.00026,0.0003,0.99991,0.99642,0.3,0.64327,26,98,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Brain,Nervous System
44011,SRR6211481,SRX3320756,SRS2626330,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 1 scar,GSM2830052,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM2830052,GSM2830052: Brain 1 scar; Danio rerio; OTHER,GSM2830052,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830052,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,B5_scar_R1.fastq.gz B5_scar_R2.fastq.gz,fastq fastq,438883452.0,3483202.0,GSM2830052 r1,0:26 1:100,A:125829044;C:139532010;G:100613706;T:72846911;N:61781,26,100,,,125829044,139532010,100613706,72846911,61781,SRX3320756,SRS2626330,SRA623333,GEO,Max Delbrück Center,2,0.00072,0.0013,0.00069,0.00011,0.99991,0.99878,0.75,0.36879,26,100,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Brain,Nervous System
66962,SRR16912780,SRX13105209,SRS11041502,SRP345473,PRJNA779441,Single Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum,PRJNA779441,Other,The optic tectum OT is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus  the OT is responsible for the reception and integration of stimuli  followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades  less is known concerning specific cell types  microcircuitry  and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however  a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single cell RNA sequencing scRNA seq to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Etcfos:Gal4;UAS:Kaede. We sequenced 13 320 cells  a 4X cellular coverage  and identified 25 putative OT cell populations. Within those cells  we identified several mature and developing neuronal populations  as well as non neuronal cell types including oligodendrocytes  microglia  and radial glia. Although most mature neurons demonstrate GABAergic activity  several glutamatergic populations are present  as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes  and computed RNA velocity to infer current and future transcriptional cell states. Finally  we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion  the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge  this is the first time scRNA seq has been applied to explore the OT alone and in depth.,,,,,Optic Tectum Run 2,,strain:y304Etcfos:Gal4; UAS:Kaede|age:7dpf|dev stage:Larval|sex:Unknown|tissue:Kaede+ midbrain cells|sample type:Methanol fixed FAC sorted cells|Run Number:2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: larval optic tectum,18798R,18798R,10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP345473,,,18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_I1_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_I2_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_R1_001.fastq.gz 18798X1_210405_A00421_0312_BHYYKVDSXY_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,51241551174.0,258795713.0,18798X1 210405 A00421 0312 BHYYKVDSXY S1 L004 I1 001.fastq.gz,0:10 1:10 2:28 3:150,A:11347233208;C:8190548246;G:9193124724;T:10088035538;N:415234,10,10,28,150,11347233208,8190548246,9193124724,10088035538,415234,SRX13105209,SRS11041502,SRA1327223,Brigham Young University|Cell Biology and Physiology,Brigham Young University,1,0.87747,,0.31462,,0.80095,,0.57402,,150,,B,,usable mapping rate,illumina,novaseq_era,3prime,other,unknown,sc,single_cell_droplet,10x,,United States,2021-11-10,Larval,Larval,Brain,Nervous System
66963,SRR16912781,SRX13105208,SRS11041501,SRP345473,PRJNA779441,Single Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum,PRJNA779441,Other,The optic tectum OT is a multilaminated midbrain structure that acts as the primary retinorecipient in the zebrafish brain. Homologous to the mammalian superior colliculus  the OT is responsible for the reception and integration of stimuli  followed by elicitation of salient behavioral responses. While the OT has been the focus of functional experiments for decades  less is known concerning specific cell types  microcircuitry  and their individual functions within the OT. Recent efforts have contributed substantially to the knowledge of tectal cell types; however  a comprehensive cell catalog is incomplete. Here we contribute to this growing effort by applying single cell RNA sequencing scRNA seq to characterize the transcriptomic profiles of tectal cells labeled by the transgenic enhancer trap line y304Etcfos:Gal4;UAS:Kaede. We sequenced 13 320 cells  a 4X cellular coverage  and identified 25 putative OT cell populations. Within those cells  we identified several mature and developing neuronal populations  as well as non neuronal cell types including oligodendrocytes  microglia  and radial glia. Although most mature neurons demonstrate GABAergic activity  several glutamatergic populations are present  as well as one glycinergic population. We also conducted Gene Ontology analysis to identify enriched biological processes  and computed RNA velocity to infer current and future transcriptional cell states. Finally  we conducted in situ hybridization to validate our bioinformatic analyses and spatially map select clusters. In conclusion  the larval zebrafish OT is a complex structure containing at least 25 transcriptionally distinct cell populations. To our knowledge  this is the first time scRNA seq has been applied to explore the OT alone and in depth.,,,,,Optic Tectum Run 1,,strain:y304Etcfos:Gal4; UAS:Kaede|age:7dpf|dev stage:Larval|sex:Unknown|tissue:Kaede+ midbrain cells|sample type:Methanol fixed FAC sorted cells|Run Number:1|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: larval optic tectum,18507R,18507R,10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP345473,,,18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_I1_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_I2_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_R1_001.fastq.gz 18507X1_201113_A00421_0256_BHLY3JDSXY_S5_L003_R2_001.fastq.gz,fastq fastq fastq fastq,64682907300.0,326681350.0,18507X1 201113 A00421 0256 BHLY3JDSXY S5 L003 I1 001.fastq.gz,0:10 1:10 2:28 3:150,A:14518921141;C:9982364575;G:11381145187;T:13119455374;N:316223,10,10,28,150,14518921141,9982364575,11381145187,13119455374,316223,SRX13105208,SRS11041501,SRA1327223,Brigham Young University|Cell Biology and Physiology,Brigham Young University,1,0.87166,,0.34827,,0.82298,,0.60301,,150,,B,,usable mapping rate,illumina,novaseq_era,3prime,other,unknown,sc,single_cell_droplet,10x,,United States,2021-11-11,Larval,Larval,Brain,Nervous System
67053,SRR17026704,SRX13216734,SRS11142397,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,I,C KO,CK3,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CK3,CK3,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CK3_R1.fastq.gz CK3_R2.fastq.gz,fastq fastq,7416029478.0,24556389.0,CK3 R1.fastq.gz,0:151 1:151,A:2009338296;C:1698532048;G:1730113268;T:1978028729;N:17137,151,151,,,2009338296,1698532048,1730113268,1978028729,17137,SRX13216734,SRS11142397,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.9353,0.93623,0.08453,0.08527,0.71551,0.71618,0.49695,0.49568,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67054,SRR17026705,SRX13216733,SRS11142398,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,H,C KO,CK2,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CK2,CK2,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CK2_R1.fastq.gz CK2_R2.fastq.gz,fastq fastq,7590854258.0,25135279.0,CK2 R1.fastq.gz,0:151 1:151,A:2041517653;C:1754766573;G:1784738177;T:2009814138;N:17717,151,151,,,2041517653,1754766573,1784738177,2009814138,17717,SRX13216733,SRS11142398,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.93771,0.93725,0.07877,0.07858,0.71739,0.71747,0.49923,0.49556,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67055,SRR17026706,SRX13216732,SRS11142395,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,G,C KO,CK1,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CK1,CK1,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CK1_R1.fastq.gz CK1_R2.fastq.gz,fastq fastq,6970012926.0,23079513.0,CK1 R1.fastq.gz,0:151 1:151,A:1881234941;C:1605828944;G:1630994283;T:1851938444;N:16314,151,151,,,1881234941,1605828944,1630994283,1851938444,16314,SRX13216732,SRS11142395,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.93953,0.93921,0.07632,0.07583,0.71853,0.71859,0.49982,0.50306,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67056,SRR17026707,SRX13216731,SRS11142393,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,F,C Male,CM3,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CM3,CM3,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CM3_R1.fastq.gz CM3_R2.fastq.gz,fastq fastq,6554074064.0,21702232.0,CM3 R1.fastq.gz,0:151 1:151,A:1751561620;C:1527225291;G:1555097615;T:1720174098;N:15440,151,151,,,1751561620,1527225291,1555097615,1720174098,15440,SRX13216731,SRS11142393,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.94488,0.9451,0.06843,0.0681,0.72829,0.72817,0.50055,0.5012,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67057,SRR17026708,SRX13216730,SRS11142392,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,E,C Male,CM2,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CM2,CM2,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CM2_R1.fastq.gz CM2_R2.fastq.gz,fastq fastq,6775620962.0,22435831.0,CM2 R1.fastq.gz,0:151 1:151,A:1822502937;C:1567415362;G:1594060885;T:1791625779;N:15999,151,151,,,1822502937,1567415362,1594060885,1791625779,15999,SRX13216730,SRS11142392,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.94019,0.94062,0.07513,0.0751,0.71847,0.71922,0.4841,0.49018,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67058,SRR17026709,SRX13216729,SRS11142394,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,D,C Male,CM1,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:male|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CM1,CM1,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CM1_R1.fastq.gz CM1_R2.fastq.gz,fastq fastq,7547878148.0,24992974.0,CM1 R1.fastq.gz,0:151 1:151,A:2049794521;C:1727106839;G:1752167931;T:2018790733;N:18124,151,151,,,2049794521,1727106839,1752167931,2018790733,18124,SRX13216729,SRS11142394,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.93694,0.9365,0.08422,0.08378,0.71658,0.71654,0.49676,0.4978,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67059,SRR17026710,SRX13216728,SRS11142390,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,C,C Female,CF3,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:female|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CF3,CF3,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CF3_R1.fastq.gz CF3_R2.fastq.gz,fastq fastq,6471047922.0,21427311.0,CF3 R1.fastq.gz,0:151 1:151,A:1715522671;C:1521915743;G:1546665820;T:1686928589;N:15099,151,151,,,1715522671,1521915743,1546665820,1686928589,15099,SRX13216728,SRS11142390,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.94618,0.94583,0.05607,0.05556,0.73184,0.73158,0.5025,0.50567,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67060,SRR17026711,SRX13216727,SRS11142391,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,B,C Female,CF2,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:female|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CF2,CF2,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CF2_R1.fastq.gz CF2_R2.fastq.gz,fastq fastq,7818271432.0,25888316.0,CF2 R1.fastq.gz,0:151 1:151,A:2101158671;C:1810803776;G:1839717812;T:2066573107;N:18066,151,151,,,2101158671,1810803776,1839717812,2066573107,18066,SRX13216727,SRS11142391,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.93945,0.93943,0.06978,0.06927,0.72034,0.71932,0.49266,0.48929,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
67061,SRR17026712,SRX13216726,SRS11142389,SRP347573,PRJNA783180,Zebrafish  Brain,PRJNA783180,Other,Zebrafish Brain,,,A,C Female,CF1,,strain:missing|isolate:missing|breed:missing|age:90dpf|sex:female|tissue:Brain|biomaterial provider:missing|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:missing|cell subtype:missing|cell type:missing|collected by:missing|collection date:missing|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|geo loc name:missing|growth protocol:missing|health state:missing|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish Brain,CF1,CF1,Sex,,,RNA-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP347573,,,CF1_R2.fastq.gz CF1_R1.fastq.gz,fastq fastq,7448526188.0,24663994.0,CF1 R1.fastq.gz,0:151 1:151,A:1995220552;C:1730768595;G:1757104436;T:1965415170;N:17435,151,151,,,1995220552,1730768595,1757104436,1965415170,17435,SRX13216726,SRS11142389,SRA1334340,Chinese Academy of Sciences|Institute of Hydrology,Chinese Academy of Sciences,2,0.9424,0.94214,0.07069,0.07015,0.71934,0.72019,0.49122,0.49476,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-11-24,Adult,Adult,Brain,Nervous System
68382,SRR17720609,SRX13883476,SRS11752245,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m7G Normoxia IP,GSM5832287,,source name:zebrafish brain tissue|tissue:brain,m7G Normoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832287,GSM5832287: m7G Normoxia IP; Danio rerio; OTHER,GSM5832287 r1,GSM5832287,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m7G_Normoxia_IP_R1.fastq.gz m7G_Normoxia_IP_R2.fastq.gz,fastq fastq,6634104000.0,22113680.0,GSM5832287 r1,0:150 1:150,A:1396464650;C:1688319426;G:2250091870;T:1299109891;N:118163,150,150,,,1396464650,1688319426,2250091870,1299109891,118163,SRX13883476,SRS11752245,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.9266,0.92801,0.07275,0.06866,0.89964,0.90601,0.65995,0.75535,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68383,SRR17720610,SRX13883475,SRS11752244,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m7G Normoxia Input,GSM5832286,,source name:zebrafish brain tissue|tissue:brain,m7G Normoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832286,GSM5832286: m7G Normoxia Input; Danio rerio; OTHER,GSM5832286 r1,GSM5832286,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m7G_Normoxia_Input_R1.fastq.gz m7G_Normoxia_Input_R2.fastq.gz,fastq fastq,6839977800.0,22799926.0,GSM5832286 r1,0:150 1:150,A:1986780958;C:1411210049;G:1509902094;T:1932043482;N:41217,150,150,,,1986780958,1411210049,1509902094,1932043482,41217,SRX13883475,SRS11752244,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.89709,0.89888,0.21747,0.21725,0.70021,0.69936,0.50469,0.51865,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68384,SRR17720611,SRX13883474,SRS11752243,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m7G Hypoxia IP,GSM5832285,,source name:zebrafish brain tissue|tissue:brain,m7G Hypoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832285,GSM5832285: m7G Hypoxia IP; Danio rerio; OTHER,GSM5832285 r1,GSM5832285,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m7G_Hypoxia_IP_R1.fastq.gz m7G_Hypoxia_IP_R2.fastq.gz,fastq fastq,7282575000.0,24275250.0,GSM5832285 r1,0:150 1:150,A:1512757767;C:1913587260;G:2472336371;T:1383764924;N:128678,150,150,,,1512757767,1913587260,2472336371,1383764924,128678,SRX13883474,SRS11752243,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.94526,0.9467,0.05248,0.05071,0.91946,0.91981,0.69303,0.78448,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68385,SRR17720612,SRX13883473,SRS11752241,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m7G Hypoxia Input,GSM5832284,,source name:zebrafish brain tissue|tissue:brain,m7G Hypoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832284,GSM5832284: m7G Hypoxia Input; Danio rerio; OTHER,GSM5832284 r1,GSM5832284,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m7G_Hypoxia_Input_R1.fastq.gz m7G_Hypoxia_Input_R2.fastq.gz,fastq fastq,7492311600.0,24974372.0,GSM5832284 r1,0:150 1:150,A:2208863421;C:1521950436;G:1608371217;T:2153082842;N:43684,150,150,,,2208863421,1521950436,1608371217,2153082842,43684,SRX13883473,SRS11752241,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.89264,0.89479,0.23239,0.23163,0.70496,0.70311,0.51741,0.52135,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68386,SRR17720613,SRX13883472,SRS11752242,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m6A Normoxia IP,GSM5832283,,source name:zebrafish brain tissue|tissue:brain,m6A Normoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832283,GSM5832283: m6A Normoxia IP; Danio rerio; OTHER,GSM5832283 r1,GSM5832283,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,,m6A_Normoxia_IP_R1.fastq.gz m6A_Normoxia_IP_R2.fastq.gz,fastq fastq,6583667700.0,21945559.0,GSM5832283 r1,0:150 1:150,A:1750230540;C:1500991424;G:1592129260;T:1740287575;N:28901,150,150,,,1750230540,1500991424,1592129260,1740287575,28901,SRX13883472,SRS11752242,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.87682,0.87986,0.18203,0.17239,0.74671,0.7472,0.55638,0.55861,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68387,SRR17720614,SRX13883471,SRS11752240,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m6A Normoxia Input,GSM5832282,,source name:zebrafish brain tissue|tissue:brain,m6A Normoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832282,GSM5832282: m6A Normoxia Input; Danio rerio; OTHER,GSM5832282 r1,GSM5832282,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m6A_Normoxia_Input_R1.fastq.gz m6A_Normoxia_Input_R2.fastq.gz,fastq fastq,6314076000.0,21046920.0,GSM5832282 r1,0:150 1:150,A:1815907910;C:1329572814;G:1378464668;T:1790102301;N:28307,150,150,,,1815907910,1329572814,1378464668,1790102301,28307,SRX13883471,SRS11752240,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.91754,0.91835,0.21273,0.20993,0.69702,0.69625,0.53456,0.53763,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68388,SRR17720615,SRX13883470,SRS11752239,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m6A Hypoxia IP,GSM5832281,,source name:zebrafish brain tissue|tissue:brain,m6A Hypoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832281,GSM5832281: m6A Hypoxia IP; Danio rerio; OTHER,GSM5832281 r1,GSM5832281,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,,m6A_Hypoxia_IP_R1.fastq.gz m6A_Hypoxia_IP_R2.fastq.gz,fastq fastq,6490349100.0,21634497.0,GSM5832281 r1,0:150 1:150,A:1714144102;C:1483635762;G:1606044832;T:1686496024;N:28380,150,150,,,1714144102,1483635762,1606044832,1686496024,28380,SRX13883470,SRS11752239,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.87598,0.88161,0.16783,0.16105,0.74588,0.74568,0.55361,0.55307,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68389,SRR17720616,SRX13883469,SRS11752237,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m6A Hypoxia Input,GSM5832280,,source name:zebrafish brain tissue|tissue:brain,m6A Hypoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832280,GSM5832280: m6A Hypoxia Input; Danio rerio; OTHER,GSM5832280 r1,GSM5832280,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m6A_Hypoxia_Input_R1.fastq.gz m6A_Hypoxia_Input_R2.fastq.gz,fastq fastq,7054483800.0,23514946.0,GSM5832280 r1,0:150 1:150,A:2000164754;C:1513377207;G:1570441784;T:1970468107;N:31948,150,150,,,2000164754,1513377207,1570441784,1970468107,31948,SRX13883469,SRS11752237,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.91916,0.91997,0.21403,0.21158,0.69716,0.69503,0.52616,0.51982,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68390,SRR17720617,SRX13883468,SRS11752238,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m5C Normoxia IP,GSM5832279,,source name:zebrafish brain tissue|tissue:brain,m5C Normoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832279,GSM5832279: m5C Normoxia IP; Danio rerio; OTHER,GSM5832279 r1,GSM5832279,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m5C_Normoxia_IP_R1.fastq.gz m5C_Normoxia_IP_R2.fastq.gz,fastq fastq,7385723100.0,24619077.0,GSM5832279 r1,0:150 1:150,A:1779838658;C:1853060139;G:2010257354;T:1742536078;N:30871,150,150,,,1779838658,1853060139,2010257354,1742536078,30871,SRX13883468,SRS11752238,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.88617,0.87633,0.42619,0.41974,0.71792,0.74016,0.69827,0.68649,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68391,SRR17720618,SRX13883467,SRS11752236,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m5C Normoxia Input,GSM5832278,,source name:zebrafish brain tissue|tissue:brain,m5C Normoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832278,GSM5832278: m5C Normoxia Input; Danio rerio; OTHER,GSM5832278 r1,GSM5832278,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m5C_Normoxia_Input_R1.fastq.gz m5C_Normoxia_Input_R2.fastq.gz,fastq fastq,6594811500.0,21982705.0,GSM5832278 r1,0:150 1:150,A:1941068575;C:1341378672;G:1414823713;T:1897501503;N:39037,150,150,,,1941068575,1341378672,1414823713,1897501503,39037,SRX13883467,SRS11752236,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.89423,0.89602,0.22595,0.2243,0.70212,0.70112,0.52954,0.52253,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68392,SRR17720619,SRX13883466,SRS11752235,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m5C Hypoxia IP,GSM5832277,,source name:zebrafish brain tissue|tissue:brain,m5C Hypoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832277,GSM5832277: m5C Hypoxia IP; Danio rerio; OTHER,GSM5832277 r1,GSM5832277,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m5C_Hypoxia_IP_R1.fastq.gz m5C_Hypoxia_IP_R2.fastq.gz,fastq fastq,7837067100.0,26123557.0,GSM5832277 r1,0:150 1:150,A:1881167242;C:1973697370;G:2143523979;T:1838645554;N:32955,150,150,,,1881167242,1973697370,2143523979,1838645554,32955,SRX13883466,SRS11752235,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.87593,0.87108,0.45438,0.45093,0.71664,0.7321,0.67861,0.69742,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68393,SRR17720620,SRX13883465,SRS11752233,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m5C Hypoxia Input,GSM5832276,,source name:zebrafish brain tissue|tissue:brain,m5C Hypoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832276,GSM5832276: m5C Hypoxia Input; Danio rerio; OTHER,GSM5832276 r1,GSM5832276,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m5C_Hypoxia_Input_R1.fastq.gz m5C_Hypoxia_Input_R2.fastq.gz,fastq fastq,8696183100.0,28987277.0,GSM5832276 r1,0:150 1:150,A:2564166903;C:1771446935;G:1858965930;T:2501551942;N:51390,150,150,,,2564166903,1771446935,1858965930,2501551942,51390,SRX13883465,SRS11752233,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.89379,0.89585,0.23898,0.23828,0.70272,0.70278,0.52965,0.50047,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68394,SRR17720621,SRX13883464,SRS11752234,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m1A Normoxia IP,GSM5832275,,source name:zebrafish brain tissue|tissue:brain,m1A Normoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832275,GSM5832275: m1A Normoxia IP; Danio rerio; OTHER,GSM5832275 r1,GSM5832275,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m1A_Normoxia_IP_R1.fastq.gz m1A_Normoxia_IP_R2.fastq.gz,fastq fastq,6882734400.0,22942448.0,GSM5832275 r1,0:150 1:150,A:1321946139;C:1977632664;G:2310916241;T:1272200359;N:38997,150,150,,,1321946139,1977632664,2310916241,1272200359,38997,SRX13883464,SRS11752234,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.88367,0.88951,0.09774,0.09525,0.86395,0.86401,0.70125,0.74894,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68395,SRR17720622,SRX13883463,SRS11752232,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m1A Normoxia Input,GSM5832274,,source name:zebrafish brain tissue|tissue:brain,m1A Normoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832274,GSM5832274: m1A Normoxia Input; Danio rerio; OTHER,GSM5832274 r1,GSM5832274,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m1A_Normoxia_Input_R1.fastq.gz m1A_Normoxia_Input_R2.fastq.gz,fastq fastq,7374452700.0,24581509.0,GSM5832274 r1,0:150 1:150,A:1511389847;C:2082118937;G:2325922232;T:1454979400;N:42284,150,150,,,1511389847,2082118937,2325922232,1454979400,42284,SRX13883463,SRS11752232,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.94589,0.94385,0.18226,0.18222,0.80878,0.8102,0.73686,0.71921,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68396,SRR17720623,SRX13883462,SRS11752231,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m1A Hypoxia IP,GSM5832273,,source name:zebrafish brain tissue|tissue:brain,m1A Hypoxia IP,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832273,GSM5832273: m1A Hypoxia IP; Danio rerio; OTHER,GSM5832273 r1,GSM5832273,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m1A_Hypoxia_IP_R1.fastq.gz m1A_Hypoxia_IP_R2.fastq.gz,fastq fastq,4861573800.0,16205246.0,GSM5832273 r1,0:150 1:150,A:927063480;C:1355342107;G:1698345464;T:880801957;N:20792,150,150,,,927063480,1355342107,1698345464,880801957,20792,SRX13883462,SRS11752231,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.8575,0.86165,0.10013,0.09909,0.87249,0.87221,0.72225,0.66629,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
68397,SRR17720624,SRX13883461,SRS11752229,SRP356476,PRJNA800053,Mapping the m1A  m5C  m6A and m7G Methylation Atlas in Zebrafish Brains under Hypoxic Conditions by MeRIP seq,GSE194284,Other,The epigenetic modifications play important regulatory roles in tissue development  maintenance of physiological functions and pathological process. RNA methylations  including newly identified m1A  m5C  m6A and m7G  are important epigenetic modifications. However  how these modifications are distributed in the transcriptome of vertebrate brains and whether their abundance is altered under pathological conditions are still poorly understood. In this study  we chose the model animal of zebrafish to conduct a systematic study to investigate the mRNA methylation atlas in the brain. By performing unbiased analyses of the m1A  m5C  m6A and m7G methylation of mRNA  we found that within the whole brain transcriptome  with the increase of the gene expression levels  the overall level of each of these four modifications on the related genes was also progressively increased. Further bioinformatics analysis indicated that the zebrafish brain has an abundance of m1A modifications. In the hypoxia treated zebrafish brains  the proportion of m1A is decreased  affecting the RNA splicing and zebrafish endogenous retroviruses. Our study presents the first comprehensive atlas of m1A  m5C  m6A and m7G in the epitranscriptome of the zebrafish brain and reveals the distribution of these modifications in mRNA under hypoxic conditions. These data provide an invaluable resource for further research on the involvement of m1A  m5C  m6A and m7G in the regulation of miRNA and repeat elements in vertebrates  and provide new thoughts to study the brain hypoxic injury on the aspect of epitranscriptome. Overall design: For each normoxia control and hypoxia experimental group  10 adult male zebrafish 3 mpf 4 mpf were chosen for the analyses. Three repeats of each experiment were performed and totally 30 fishes per group were collected. The brain tissues around 0.02 g per brain were then stored for further analysis in liquid nitrogen. For each analysis m1A  m5C  m6A  m7G and RNA Seq  the normoxia group and hypoxic group each consisted of 30 mixed brain tissues were analyzed parallelly by RNA seq and MeRIP Seq.,,pubmed:35135476,,m1A Hypoxia Input,GSM5832272,,source name:zebrafish brain tissue|tissue:brain,m1A Hypoxia Input,Paired end reads were harvested from an Illumina NovaSeq 6000 sequencer Cutadapt v1.9.3  command line software  was used to identify and trim 3’ adapter and low quality bases for rawdata. The clean data were mapped to the reference genome GRCz11 using Hisat2 software v2.0.4. For RNA seq: Guiding by the Ensembl GTF gene annotation file  Cuffdiff software part of cufflinks was used to obtain the gene level FPKM as the expression profiles of mRNA  fold change and p value were calculated based on FPKM For MeRIP seq: To identify the methylated sites on RNAs peaks  MACS software was utilized. Differentially methylated sites were identified by diffReps. The motif predictions of MeRIP Seq data were performed by utilizing a Perl script  findMotifGenome.pl  from HOMER software. Genome build: GRCz11 Supplementary files format and content: Gene expression valuesFPKM and Counts and methylated sites,zebrafish brain tissue,Adult wild type zebrafish Danio rerio were bred according to standard methods. For hypoxia treatment  we followed settings established in a previously published protocolYu et al 2011 with modified conditions. Briefly  zebrafish were transferred into a 1 L chamber containing 800 mL predeoxidated water O2: 0.3 0.4 mg/L. Oxygen in the water was then exhausted through the application of 8 L/min nitrogen until the dissolved oxygen value in the water was approximately 0.4 0.6 mg/L. Nitrogen 1 L/min was used to maintain the dissolved oxygen level in the water. post approximately 5 minutes  when the fish became motionless  the zebrafish brain were dissected on ice post anesthetizing to obtain brain tissues. The brain tissues were stored for further analysis in liquid nitrogen.,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,tissue:brain,GSM5832272,GSM5832272: m1A Hypoxia Input; Danio rerio; OTHER,GSM5832272 r1,GSM5832272,1,Ribo Zero rRNA Removal Kits Illumina  San Diego  CA  USA For RNA seq : TruSeq Stranded Total RNA Library Prep Kit Illumina  San Diego  CA  USA For MeRIP seq: GenSeqTM RNA IP Kit GenSeq Inc.  China and NEBNext® Ultra II Directional RNA Library Prep Kit New England Biolabs  Inc.  USA RNA seq and MeRIP seq,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP356476,,loader:fastq load.py,m1A_Hypoxia_Input_R1.fastq.gz m1A_Hypoxia_Input_R2.fastq.gz,fastq fastq,7262130600.0,24207102.0,GSM5832272 r1,0:150 1:150,A:1553326396;C:2003023914;G:2214285414;T:1491453374;N:41502,150,150,,,1553326396,2003023914,2214285414,1491453374,41502,SRX13883461,SRS11752229,SRA1361294,Affiliated Hospital of Guangdong Medical University,Affiliated Hospital of Guangdong Medical University,2,0.94247,0.94013,0.20625,0.20507,0.80188,0.80137,0.70188,0.73891,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,nebnext,bulk,bulk,bulk,,China,2022-01-24,Adult,Adult,Brain,Nervous System
75288,SRR25598371,SRX21326033,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R6,3124R6,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F1-5_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L002_R1_001.fastq.gz 3124F1-5_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L002_R2_001.fastq.gz,fastq fastq,10700303544.0,127384566.0,3124F1 5 220322 A01563 0038 AHY3YHDRXY GCAGTATAGG GTGCACGGAA L002 R1 001.fastq.gz,0:28 1:56,A:3095737110;C:2216347626;G:2244897948;T:3142928946;N:391914,28,56,,,3095737110,2216347626,2244897948,3142928946,391914,SRX21326033,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00785,0.88899,0.00393,0.43423,0.99017,0.7486,0.36074,0.50405,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75289,SRR25598372,SRX21326032,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R5,3124R5,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F2-5_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L002_R1_001.fastq.gz 3124F2-5_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L002_R2_001.fastq.gz,fastq fastq,15103664688.0,179805532.0,3124F2 5 220322 A01563 0038 AHY3YHDRXY AACCACGCAT TAACCTGAAT L002 R1 001.fastq.gz,0:28 1:56,A:4376559806;C:3122875667;G:3166215898;T:4437453369;N:559948,28,56,,,4376559806,3122875667,3166215898,4437453369,559948,SRX21326032,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00779,0.88709,0.00398,0.43543,0.98973,0.74736,0.35685,0.49938,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75290,SRR25598373,SRX21326031,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R4,3124R4,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F3-5_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L002_R1_001.fastq.gz 3124F3-5_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L002_R2_001.fastq.gz,fastq fastq,11678915220.0,139034705.0,3124F3 5 220322 A01563 0038 AHY3YHDRXY CCCACCACAA AAGCGGAGGT L002 R1 001.fastq.gz,0:28 1:56,A:3362125535;C:2431029106;G:2460479617;T:3424857950;N:423012,28,56,,,3362125535,2431029106,2460479617,3424857950,423012,SRX21326031,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00813,0.89215,0.00415,0.42908,0.99028,0.74651,0.33376,0.49996,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75291,SRR25598374,SRX21326030,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R3,3124R3,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F1-1_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L001_R1_001.fastq.gz 3124F1-1_220322_A01563_0038_AHY3YHDRXY_GCAGTATAGG-GTGCACGGAA_L001_R2_001.fastq.gz,fastq fastq,22921793076.0,272878489.0,3124F1 1 220322 A01563 0038 AHY3YHDRXY GCAGTATAGG GTGCACGGAA L001 R1 001.fastq.gz,0:28 1:56,A:6639916156;C:4743377942;G:4802115704;T:6735725053;N:658221,28,56,,,6639916156,4743377942,4802115704,6735725053,658221,SRX21326030,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00785,0.88789,0.00408,0.43253,0.99003,0.74722,0.39124,0.51078,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75292,SRR25598375,SRX21326029,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R2,3124R2,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F2-1_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L001_R1_001.fastq.gz 3124F2-1_220322_A01563_0038_AHY3YHDRXY_AACCACGCAT-TAACCTGAAT_L001_R2_001.fastq.gz,fastq fastq,32435983776.0,386142664.0,3124F2 1 220322 A01563 0038 AHY3YHDRXY AACCACGCAT TAACCTGAAT L001 R1 001.fastq.gz,0:28 1:56,A:9417269653;C:6700846098;G:6786259472;T:9530672341;N:936212,28,56,,,9417269653,6700846098,6786259472,9530672341,936212,SRX21326029,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00815,0.88581,0.00428,0.43686,0.98957,0.74704,0.35752,0.50656,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75293,SRR25598376,SRX21326028,SRS18572181,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3124R,,breed:wildtype|age:6 mpf|dev stage:adult|collection date:2022 03 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3124R1,3124R1,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3124F3-1_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L001_R1_001.fastq.gz 3124F3-1_220322_A01563_0038_AHY3YHDRXY_CCCACCACAA-AAGCGGAGGT_L001_R2_001.fastq.gz,fastq fastq,24948540624.0,297006436.0,3124F3 1 220322 A01563 0038 AHY3YHDRXY CCCACCACAA AAGCGGAGGT L001 R1 001.fastq.gz,0:28 1:56,A:7193047366;C:5189304192;G:5248299831;T:7317170808;N:718427,28,56,,,7193047366,5189304192,5248299831,7317170808,718427,SRX21326028,SRS18572181,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00769,0.89098,0.00387,0.42984,0.99038,0.74878,0.30434,0.49663,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System
75294,SRR25598377,SRX21326027,SRS18572180,SRP454447,PRJNA964500,Danio rerio telencephalon sequencing,PRJNA964500,Whole Genome Sequencing,We aimed to characterize different regions and cell types in the telencephalon of zebrafish D. rerio.,,,the telencephalon of two fish was extracted and dissociated for preparing scRNA seq libraries,,3065R,,breed:wildtype|age:8 mpf|dev stage:adult|collection date:2022 01 11|geo loc name:Switzerland|sex:male|tissue:telencephalon|biomaterial provider:Rainer Friedrich|collected by:Lukas Anneser|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: adult telencephalon,3065R,3065R,Single cell suspension from adult Danio rerio telencephalon. Library prepared with 10X Genomics v3 reagents.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP454447,,,3065F1-1_220118_NB501735_0823_AH3HHLBGXL_GTAACATG-NoIndex_L000_R1_001.fastq.gz 3065F1-1_220118_NB501735_0823_AH3HHLBGXL_GTAACATG-NoIndex_L000_R2_001.fastq.gz,fastq fastq,35548236948.0,423193297.0,3065F1 1 220118 NB501735 0823 AH3HHLBGXL GTAACATG NoIndex L000 R1 001.fastq.gz,0:28 1:56,A:10224422089;C:7414175917;G:7794098189;T:10109777968;N:5762785,28,56,,,10224422089,7414175917,7794098189,10109777968,5762785,SRX21326027,SRS18572180,SRA1690085,Friedrich Miescher Institute for Biomedical Research|Neurobiology,Friedrich Miescher Institute for Biomedical Research,2,0.00913,0.90845,0.00399,0.3776,0.99024,0.75455,0.32653,0.50632,28,56,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Switzerland,2023-08-10,Adult,Adult,Brain,Nervous System