{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation_coarse = \"Nervous System\"", "rows": [[7950, "ERR015567", "ERX005930", "ERS000089", "ERP000263", "PRJEB2208", "Zebrafish gene three prime end pull down for genome annotation", "E-MTAB-308", "Transcriptome Analysis", null, null, null, "RNA extracted from male adult zebrafish head", null, "SAMEA708835", "SC", "ENA FIRST PUBLIC:2010 02 26T10:44:13Z|ENA LAST UPDATE:2018 03 08T15:51:30Z|External Id:SAMEA708835|INSDC center name:SC|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:51:30Z|INSDC status:public|Submitter Id:ZF male head sample1|common name:zebrafish|sample name:ZF male head sample1|scientific name:Danio rerio|sex:male|strain:Tuebingen", null, null, null, null, null, null, null, null, "Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation", "E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert", "Zebrafish adult male head mRNA three prime end", "Zebrafish gene three prime end pull down for genome annotation", "20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl.   RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin  magnetic beads.   post washing by pull down on a magnet  the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB.   post further washing  the double strand cDNA was released from the beads with BpmI NEB.   The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp.", "Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head|Experimental Factor: SEX:male", "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP000263", "Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation", "ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16", "3444_7.srf", "srf", 1384012896.0, 9105348.0, "E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert", "0:76 1:76", "A:369912216;C:306963547;G:292249178;T:392053840;N:22834115", 76, 76, null, null, 369912216, 306963547, 292249178, 392053840, 22834115, "ERX005930", "ERS000089", "ERA010603", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.95932, 0.96084, 0.20719, 0.21321, 0.73959, 0.74763, 0.47227, 0.48033, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "3prime", "other", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2010-02-26", "Adult", "Adult", "Head", "Nervous System"], [9927, "ERR4321734", "ERX4268592", "ERS4808149", "ERP122765", "PRJEB39269", "Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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/\u00df 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/\u00df 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", null, "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", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u03b2 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/\u03b2 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", null, "ERP122765", "NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/\u00ce\u00b2 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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "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, null, null, 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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  cirbpb scars", "GSM7875190", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz", "fastq fastq", 157576336.0, 949552.0, "GSM7875190 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323921", "SRS19374450", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  cfl1 scars", "GSM7875189", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz", "fastq fastq", 381453696.0, 2184402.0, "GSM7875189 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323920", "SRS19374449", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  actb2 scars", "GSM7875188", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz", "fastq fastq", 491682118.0, 2851156.0, "GSM7875188 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323919", "SRS19374448", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  actb1 scars", "GSM7875187", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz", "fastq fastq", 390405832.0, 2283319.0, "GSM7875187 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323918", "SRS19374446", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Brain 23   telencephalon  Notch inhibition  scSLAMseq", "GSM7875186", null, "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 \u00b5M 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 \u00b5l 100 mM IAA to 800 \u00b5l 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 \u00b5m 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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l 100 mM IAA to 800 \u00b5l 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 \u00b5m 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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "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, null, null, 18682905645, 13783082970, 14751373116, 15161083446, 14013393, "SRX22323917", "SRS19374447", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Brain 22   telencephalon  control  scSLAMseq", "GSM7875185", null, "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 \u00b5l 100 mM IAA to 800 \u00b5l 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 \u00b5m 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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l 100 mM IAA to 800 \u00b5l 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 \u00b5m 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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "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, null, null, 18600519530, 12714987967, 14147370465, 14316863915, 13372613, "SRX22323916", "SRS19374445", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep2  ube2e1 scars", "GSM7875196", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz", "fastq fastq", 213092161.0, 1190459.0, "GSM7875196 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323897", "SRS19374426", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep2  rpl39 scars", "GSM7875195", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz", "fastq fastq", 1023403502.0, 5717338.0, "GSM7875195 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323896", "SRS19374425", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep2  cirbpb scars", "GSM7875194", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz", "fastq fastq", 276120388.0, 1542572.0, "GSM7875194 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323895", "SRS19374424", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep2  cfl1 scars", "GSM7875193", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469552", null, "loader:fastq load.py", "lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz", "fastq fastq", 791318009.0, 4420771.0, "GSM7875193 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323894", "SRS19374423", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  ube2e1 scars", "GSM7875192", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz", "fastq fastq", 99407618.0, 601781.0, "GSM7875192 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323893", "SRS19374421", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "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.", null, "pubmed:38365956", null, "Lineage tracing rep1  rpl39 scars", "GSM7875191", null, "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", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "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 \u00b5l of HBSS glucose solution and dissocated with 15 \u00b5l of 0.05% trypsin EDTA Gibco for 30 minutes at 37\u00b0C with intermittent mixing. The disociation was stopped by addition of 750 \u00b5l of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4\u00b0C. The sample was filtered through a 100 \u00b5m filter  washed with cold HBSS and resuspended in 100 200 \u00b5l HBSS with 0.05% BSA  then filtered through a 35 \u00b5m 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.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP469552", null, "loader:fastq load.py", "lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz", "fastq fastq", 401898718.0, 2276836.0, "GSM7875191 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX22323892", "SRS19374422", "SRA1743007", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Center for Molecular Medicine", "Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-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", null, "Germany", "2023-10-31", "Adult", "Adult", "Brain", "Nervous System"], [34712, "SRR32232924", "SRX27573024", "SRS23984677", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05H", "GSM8775334", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 H05|rtindex:TTCGCCTCCA|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05H", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 H05|rtindex:TTCGCCTCCA|genotype:GAL4 replicate2", "GSM8775334", "GSM8775334: Well P1 05H; Danio rerio; OTHER", "GSM8775334 r1", "GSM8775334", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05H.R2.fastq.gz P1-05H_S40_I1_001.fastq.gz P1-05H.R1.fastq.gz", "fastq fastq fastq", 828.0, 9.0, "GSM8775334 r1", "0:34 1:48 2:10", "A:210;C:74;G:47;T:101;N:0", 34, 48, 10, null, 210, 74, 47, 101, 0, "SRX27573024", "SRS23984677", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34713, "SRR32232925", "SRX27573023", "SRS23984676", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05G", "GSM8775333", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G05|rtindex:TTACCTCGAC|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G05|rtindex:TTACCTCGAC|genotype:GAL4 replicate2", "GSM8775333", "GSM8775333: Well P1 05G; Danio rerio; OTHER", "GSM8775333 r1", "GSM8775333", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05G.R1.fastq.gz P1-05G.R2.fastq.gz P1-05G_S39_I1_001.fastq.gz", "fastq fastq fastq", 3345856.0, 36368.0, "GSM8775333 r1", "0:34 1:48 2:10", "A:602824;C:246794;G:422064;T:471661;N:2321", 34, 48, 10, null, 602824, 246794, 422064, 471661, 2321, "SRX27573023", "SRS23984676", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34714, "SRR32232926", "SRX27573022", "SRS23984675", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05F", "GSM8775332", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F05|rtindex:CCATTATCTA|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F05|rtindex:CCATTATCTA|genotype:GAL4 replicate2", "GSM8775332", "GSM8775332: Well P1 05F; Danio rerio; OTHER", "GSM8775332 r1", "GSM8775332", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05F.R1.fastq.gz P1-05F.R2.fastq.gz P1-05F_S38_I1_001.fastq.gz", "fastq fastq fastq", 143353940.0, 1558195.0, "GSM8775332 r1", "0:34 1:48 2:10", "A:32466011;C:9391164;G:14603239;T:18226855;N:106091", 34, 48, 10, null, 32466011, 9391164, 14603239, 18226855, 106091, "SRX27573022", "SRS23984675", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34715, "SRR32232927", "SRX27573021", "SRS23984674", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05E", "GSM8775331", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E05|rtindex:CTAGTAGTCT|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E05|rtindex:CTAGTAGTCT|genotype:GAL4 replicate2", "GSM8775331", "GSM8775331: Well P1 05E; Danio rerio; OTHER", "GSM8775331 r1", "GSM8775331", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05E.R1.fastq.gz P1-05E.R2.fastq.gz P1-05E_S37_I1_001.fastq.gz", "fastq fastq fastq", 45118824.0, 490422.0, "GSM8775331 r1", "0:34 1:48 2:10", "A:7745921;C:3203071;G:7199342;T:5360465;N:31457", 34, 48, 10, null, 7745921, 3203071, 7199342, 5360465, 31457, "SRX27573021", "SRS23984674", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34716, "SRR32232928", "SRX27573020", "SRS23984673", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05D", "GSM8775330", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D05|rtindex:AGAGAAGGTT|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D05|rtindex:AGAGAAGGTT|genotype:GAL4 replicate2", "GSM8775330", "GSM8775330: Well P1 05D; Danio rerio; OTHER", "GSM8775330 r1", "GSM8775330", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05D.R1.fastq.gz P1-05D.R2.fastq.gz P1-05D_S36_I1_001.fastq.gz", "fastq fastq fastq", 194869248.0, 2118144.0, "GSM8775330 r1", "0:34 1:48 2:10", "A:44069791;C:12867012;G:18935172;T:25657047;N:141890", 34, 48, 10, null, 44069791, 12867012, 18935172, 25657047, 141890, "SRX27573020", "SRS23984673", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34717, "SRR32232929", "SRX27573019", "SRS23984672", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05C", "GSM8775329", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C05|rtindex:TAGAGTAATA|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C05|rtindex:TAGAGTAATA|genotype:GAL4 replicate2", "GSM8775329", "GSM8775329: Well P1 05C; Danio rerio; OTHER", "GSM8775329 r1", "GSM8775329", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05C.R1.fastq.gz P1-05C.R2.fastq.gz P1-05C_S35_I1_001.fastq.gz", "fastq fastq fastq", 47118352.0, 512156.0, "GSM8775329 r1", "0:34 1:48 2:10", "A:9098221;C:3194198;G:6516993;T:5738665;N:35411", 34, 48, 10, null, 9098221, 3194198, 6516993, 5738665, 35411, "SRX27573019", "SRS23984672", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34718, "SRR32232930", "SRX27573018", "SRS23984671", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05B", "GSM8775328", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 B05|rtindex:CTTGCGCCGC|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05B", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 B05|rtindex:CTTGCGCCGC|genotype:GAL4 replicate2", "GSM8775328", "GSM8775328: Well P1 05B; Danio rerio; OTHER", "GSM8775328 r1", "GSM8775328", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05B.R1.fastq.gz P1-05B.R2.fastq.gz P1-05B_S34_I1_001.fastq.gz", "fastq fastq fastq", 664471748.0, 7222519.0, "GSM8775328 r1", "0:34 1:48 2:10", "A:146424611;C:46287832;G:64801496;T:88677718;N:489255", 34, 48, 10, null, 146424611, 46287832, 64801496, 88677718, 489255, "SRX27573018", "SRS23984671", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34719, "SRR32232931", "SRX27573017", "SRS23984670", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 05A", "GSM8775327", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 A05|rtindex:CCGAGAATCC|genotype:GAL4 replicate2|geo loc name:missing|collection date:missing", "Well P1 05A", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 A05|rtindex:CCGAGAATCC|genotype:GAL4 replicate2", "GSM8775327", "GSM8775327: Well P1 05A; Danio rerio; OTHER", "GSM8775327 r1", "GSM8775327", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-05A.R1.fastq.gz P1-05A.R2.fastq.gz P1-05A_S33_I1_001.fastq.gz", "fastq fastq fastq", 33378152.0, 362806.0, "GSM8775327 r1", "0:34 1:48 2:10", "A:5712677;C:2316258;G:5388122;T:3975276;N:22355", 34, 48, 10, null, 5712677, 2316258, 5388122, 3975276, 22355, "SRX27573017", "SRS23984670", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34720, "SRR32232932", "SRX27573016", "SRS23984669", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12H", "GSM8775389", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 H12|rtindex:TAACTGGTTA|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12H", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 H12|rtindex:TAACTGGTTA|genotype:UAS replicate3", "GSM8775389", "GSM8775389: Well P1 12H; Danio rerio; OTHER", "GSM8775389 r1", "GSM8775389", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12H.R1.fastq.gz P1-12H.R2.fastq.gz P1-12H_S96_I1_001.fastq.gz", "fastq fastq fastq", 368.0, 4.0, "GSM8775389 r1", "0:34 1:48 2:10", "A:70;C:25;G:61;T:36;N:0", 34, 48, 10, null, 70, 25, 61, 36, 0, "SRX27573016", "SRS23984669", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34721, "SRR32232933", "SRX27573015", "SRS23984668", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12G", "GSM8775388", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G12|rtindex:GGTACCGGCA|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G12|rtindex:GGTACCGGCA|genotype:UAS replicate3", "GSM8775388", "GSM8775388: Well P1 12G; Danio rerio; OTHER", "GSM8775388 r1", "GSM8775388", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12G.R1.fastq.gz P1-12G.R2.fastq.gz P1-12G_S95_I1_001.fastq.gz", "fastq fastq fastq", 11776.0, 128.0, "GSM8775388 r1", "0:34 1:48 2:10", "A:2531;C:932;G:1152;T:1529;N:0", 34, 48, 10, null, 2531, 932, 1152, 1529, 0, "SRX27573015", "SRS23984668", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34722, "SRR32232934", "SRX27573014", "SRS23984666", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12F", "GSM8775387", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F12|rtindex:CATTCGACGG|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F12|rtindex:CATTCGACGG|genotype:UAS replicate3", "GSM8775387", "GSM8775387: Well P1 12F; Danio rerio; OTHER", "GSM8775387 r1", "GSM8775387", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12F.R1.fastq.gz P1-12F.R2.fastq.gz P1-12F_S94_I1_001.fastq.gz", "fastq fastq fastq", 1012.0, 11.0, "GSM8775387 r1", "0:34 1:48 2:10", "A:192;C:67;G:130;T:139;N:0", 34, 48, 10, null, 192, 67, 130, 139, 0, "SRX27573014", "SRS23984666", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34723, "SRR32232935", "SRX27573013", "SRS23984667", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12E", "GSM8775386", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E12|rtindex:AACCATTGGA|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E12|rtindex:AACCATTGGA|genotype:UAS replicate3", "GSM8775386", "GSM8775386: Well P1 12E; Danio rerio; OTHER", "GSM8775386 r1", "GSM8775386", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12E.R1.fastq.gz P1-12E.R2.fastq.gz P1-12E_S93_I1_001.fastq.gz", "fastq fastq fastq", 512348.0, 5569.0, "GSM8775386 r1", "0:34 1:48 2:10", "A:84224;C:34420;G:85992;T:62126;N:550", 34, 48, 10, null, 84224, 34420, 85992, 62126, 550, "SRX27573013", "SRS23984667", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34724, "SRR32232936", "SRX27573012", "SRS23984665", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12D", "GSM8775385", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D12|rtindex:CGAACGCCGG|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D12|rtindex:CGAACGCCGG|genotype:UAS replicate3", "GSM8775385", "GSM8775385: Well P1 12D; Danio rerio; OTHER", "GSM8775385 r1", "GSM8775385", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12D.R1.fastq.gz P1-12D.R2.fastq.gz P1-12D_S92_I1_001.fastq.gz", "fastq fastq fastq", 14633428.0, 159059.0, "GSM8775385 r1", "0:34 1:48 2:10", "A:2133794;C:938571;G:2850027;T:1703116;N:9324", 34, 48, 10, null, 2133794, 938571, 2850027, 1703116, 9324, "SRX27573012", "SRS23984665", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34725, "SRR32232937", "SRX27573011", "SRS23984664", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12C", "GSM8775384", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C12|rtindex:GACCTTGATA|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C12|rtindex:GACCTTGATA|genotype:UAS replicate3", "GSM8775384", "GSM8775384: Well P1 12C; Danio rerio; OTHER", "GSM8775384 r1", "GSM8775384", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12C.R1.fastq.gz P1-12C.R2.fastq.gz P1-12C_S91_I1_001.fastq.gz", "fastq fastq fastq", 24830524.0, 269897.0, "GSM8775384 r1", "0:34 1:48 2:10", "A:3753240;C:1715145;G:4579242;T:2889684;N:17745", 34, 48, 10, null, 3753240, 1715145, 4579242, 2889684, 17745, "SRX27573011", "SRS23984664", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34726, "SRR32232938", "SRX27573010", "SRS23984663", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 12B", "GSM8775383", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 B12|rtindex:TGGTCAGCCA|genotype:UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 12B", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 B12|rtindex:TGGTCAGCCA|genotype:UAS replicate3", "GSM8775383", "GSM8775383: Well P1 12B; Danio rerio; OTHER", "GSM8775383 r1", "GSM8775383", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-12B.R1.fastq.gz P1-12B.R2.fastq.gz P1-12B_S90_I1_001.fastq.gz", "fastq fastq fastq", 22899628.0, 248909.0, "GSM8775383 r1", "0:34 1:48 2:10", "A:3385725;C:1544608;G:4301274;T:2699465;N:16560", 34, 48, 10, null, 3385725, 1544608, 4301274, 2699465, 16560, "SRX27573010", "SRS23984663", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34727, "SRR32232939", "SRX27573009", "SRS23984662", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08H", "GSM8775358", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 H08|rtindex:AGCTCTCCTC|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08H", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 H08|rtindex:AGCTCTCCTC|genotype:UAS replicate2", "GSM8775358", "GSM8775358: Well P1 08H; Danio rerio; OTHER", "GSM8775358 r1", "GSM8775358", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08H.R1.fastq.gz P1-08H.R2.fastq.gz P1-08H_S64_I1_001.fastq.gz", "fastq fastq fastq", 552.0, 6.0, "GSM8775358 r1", "0:34 1:48 2:10", "A:114;C:44;G:65;T:65;N:0", 34, 48, 10, null, 114, 44, 65, 65, 0, "SRX27573009", "SRS23984662", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34728, "SRR32232940", "SRX27573008", "SRS23984661", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08G", "GSM8775357", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G08|rtindex:CGGTCAAGAA|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G08|rtindex:CGGTCAAGAA|genotype:UAS replicate2", "GSM8775357", "GSM8775357: Well P1 08G; Danio rerio; OTHER", "GSM8775357 r1", "GSM8775357", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08G.R1.fastq.gz P1-08G.R2.fastq.gz P1-08G_S63_I1_001.fastq.gz", "fastq fastq fastq", 48348484.0, 525527.0, "GSM8775357 r1", "0:34 1:48 2:10", "A:8706380;C:3262708;G:7330788;T:5889373;N:36047", 34, 48, 10, null, 8706380, 3262708, 7330788, 5889373, 36047, "SRX27573008", "SRS23984661", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34729, "SRR32232941", "SRX27573007", "SRS23984660", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08F", "GSM8775356", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F08|rtindex:GATCGCTTCT|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F08|rtindex:GATCGCTTCT|genotype:UAS replicate2", "GSM8775356", "GSM8775356: Well P1 08F; Danio rerio; OTHER", "GSM8775356 r1", "GSM8775356", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08F.R1.fastq.gz P1-08F.R2.fastq.gz P1-08F_S62_I1_001.fastq.gz", "fastq fastq fastq", 55386116.0, 602023.0, "GSM8775356 r1", "0:34 1:48 2:10", "A:10289406;C:3851867;G:8139616;T:6575750;N:40465", 34, 48, 10, null, 10289406, 3851867, 8139616, 6575750, 40465, "SRX27573007", "SRS23984660", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34730, "SRR32232942", "SRX27573006", "SRS23984659", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08E", "GSM8775355", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E08|rtindex:AACTAGGCGC|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E08|rtindex:AACTAGGCGC|genotype:UAS replicate2", "GSM8775355", "GSM8775355: Well P1 08E; Danio rerio; OTHER", "GSM8775355 r1", "GSM8775355", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08E.R1.fastq.gz P1-08E.R2.fastq.gz P1-08E_S61_I1_001.fastq.gz", "fastq fastq fastq", 40465832.0, 439846.0, "GSM8775355 r1", "0:34 1:48 2:10", "A:6595819;C:2847582;G:6802285;T:4838399;N:28523", 34, 48, 10, null, 6595819, 2847582, 6802285, 4838399, 28523, "SRX27573006", "SRS23984659", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34731, "SRR32232943", "SRX27573005", "SRS23984658", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08D", "GSM8775354", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D08|rtindex:GGCTGAGCTC|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D08|rtindex:GGCTGAGCTC|genotype:UAS replicate2", "GSM8775354", "GSM8775354: Well P1 08D; Danio rerio; OTHER", "GSM8775354 r1", "GSM8775354", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08D.R1.fastq.gz P1-08D.R2.fastq.gz P1-08D_S60_I1_001.fastq.gz", "fastq fastq fastq", 33437492.0, 363451.0, "GSM8775354 r1", "0:34 1:48 2:10", "A:4392257;C:1994475;G:7440459;T:3596074;N:22383", 34, 48, 10, null, 4392257, 1994475, 7440459, 3596074, 22383, "SRX27573005", "SRS23984658", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34732, "SRR32232944", "SRX27573004", "SRS23984656", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08C", "GSM8775353", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C08|rtindex:AGAACGTCTC|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C08|rtindex:AGAACGTCTC|genotype:UAS replicate2", "GSM8775353", "GSM8775353: Well P1 08C; Danio rerio; OTHER", "GSM8775353 r1", "GSM8775353", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08C.R1.fastq.gz P1-08C.R2.fastq.gz P1-08C_S59_I1_001.fastq.gz", "fastq fastq fastq", 29029864.0, 315542.0, "GSM8775353 r1", "0:34 1:48 2:10", "A:4629476;C:2009722;G:5052427;T:3434235;N:20156", 34, 48, 10, null, 4629476, 2009722, 5052427, 3434235, 20156, "SRX27573004", "SRS23984656", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34733, "SRR32232945", "SRX27573003", "SRS23984657", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08B", "GSM8775352", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 B08|rtindex:GCCATTCTCC|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08B", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 B08|rtindex:GCCATTCTCC|genotype:UAS replicate2", "GSM8775352", "GSM8775352: Well P1 08B; Danio rerio; OTHER", "GSM8775352 r1", "GSM8775352", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08B.R1.fastq.gz P1-08B.R2.fastq.gz P1-08B_S58_I1_001.fastq.gz", "fastq fastq fastq", 7182683524.0, 78072647.0, "GSM8775352 r1", "0:34 1:48 2:10", "A:1191235462;C:707748234;G:767219572;T:1075959763;N:5324025", 34, 48, 10, null, 1191235462, 707748234, 767219572, 1075959763, 5324025, "SRX27573003", "SRS23984657", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34734, "SRR32232946", "SRX27573002", "SRS23984655", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 08A", "GSM8775351", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 A08|rtindex:TGCGGACCTA|genotype:UAS replicate2|geo loc name:missing|collection date:missing", "Well P1 08A", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 A08|rtindex:TGCGGACCTA|genotype:UAS replicate2", "GSM8775351", "GSM8775351: Well P1 08A; Danio rerio; OTHER", "GSM8775351 r1", "GSM8775351", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-08A.R1.fastq.gz P1-08A.R2.fastq.gz P1-08A_S57_I1_001.fastq.gz", "fastq fastq fastq", 33057440.0, 359320.0, "GSM8775351 r1", "0:34 1:48 2:10", "A:5780741;C:2263389;G:5259112;T:3921095;N:23023", 34, 48, 10, null, 5780741, 2263389, 5259112, 3921095, 23023, "SRX27573002", "SRS23984655", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34735, "SRR32232947", "SRX27573001", "SRS23984654", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04H", "GSM8775326", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 H04|rtindex:AGGTTAGCAT|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04H", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 H04|rtindex:AGGTTAGCAT|genotype:UAS replicate1", "GSM8775326", "GSM8775326: Well P1 04H; Danio rerio; OTHER", "GSM8775326 r1", "GSM8775326", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04H.R1.fastq.gz P1-04H.R2.fastq.gz P1-04H_S32_I1_001.fastq.gz", "fastq fastq fastq", 4048.0, 44.0, "GSM8775326 r1", "0:34 1:48 2:10", "A:877;C:264;G:476;T:495;N:0", 34, 48, 10, null, 877, 264, 476, 495, 0, "SRX27573001", "SRS23984654", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34736, "SRR32232948", "SRX27573000", "SRS23984653", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04G", "GSM8775325", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G04|rtindex:ACGAAGTCAA|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G04|rtindex:ACGAAGTCAA|genotype:UAS replicate1", "GSM8775325", "GSM8775325: Well P1 04G; Danio rerio; OTHER", "GSM8775325 r1", "GSM8775325", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04G.R1.fastq.gz P1-04G.R2.fastq.gz P1-04G_S31_I1_001.fastq.gz", "fastq fastq fastq", 16717412.0, 181711.0, "GSM8775325 r1", "0:34 1:48 2:10", "A:2534077;C:1123957;G:3093004;T:1959215;N:11875", 34, 48, 10, null, 2534077, 1123957, 3093004, 1959215, 11875, "SRX27573000", "SRS23984653", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34737, "SRR32232949", "SRX27572999", "SRS23984652", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04F", "GSM8775324", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F04|rtindex:AATCGATAAT|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F04|rtindex:AATCGATAAT|genotype:UAS replicate1", "GSM8775324", "GSM8775324: Well P1 04F; Danio rerio; OTHER", "GSM8775324 r1", "GSM8775324", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04F.R1.fastq.gz P1-04F.R2.fastq.gz P1-04F_S30_I1_001.fastq.gz", "fastq fastq fastq", 71229712.0, 774236.0, "GSM8775324 r1", "0:34 1:48 2:10", "A:13212435;C:4888655;G:10555214;T:8456988;N:50036", 34, 48, 10, null, 13212435, 4888655, 10555214, 8456988, 50036, "SRX27572999", "SRS23984652", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34738, "SRR32232950", "SRX27572998", "SRS23984651", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04E", "GSM8775323", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E04|rtindex:TAGCCGTCAT|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E04|rtindex:TAGCCGTCAT|genotype:UAS replicate1", "GSM8775323", "GSM8775323: Well P1 04E; Danio rerio; OTHER", "GSM8775323 r1", "GSM8775323", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04E.R1.fastq.gz P1-04E.R2.fastq.gz P1-04E_S29_I1_001.fastq.gz", "fastq fastq fastq", 381955388.0, 4151689.0, "GSM8775323 r1", "0:34 1:48 2:10", "A:87514409;C:25262710;G:36461600;T:49768768;N:273585", 34, 48, 10, null, 87514409, 25262710, 36461600, 49768768, 273585, "SRX27572998", "SRS23984651", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34739, "SRR32232951", "SRX27572997", "SRS23984649", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04D", "GSM8775322", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D04|rtindex:TCCGGCCTCG|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D04|rtindex:TCCGGCCTCG|genotype:UAS replicate1", "GSM8775322", "GSM8775322: Well P1 04D; Danio rerio; OTHER", "GSM8775322 r1", "GSM8775322", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04D.R1.fastq.gz P1-04D.R2.fastq.gz P1-04D_S28_I1_001.fastq.gz", "fastq fastq fastq", 57109552.0, 620756.0, "GSM8775322 r1", "0:34 1:48 2:10", "A:11045441;C:3910161;G:7896770;T:6905332;N:38584", 34, 48, 10, null, 11045441, 3910161, 7896770, 6905332, 38584, "SRX27572997", "SRS23984649", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34740, "SRR32232952", "SRX27572996", "SRS23984650", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04C", "GSM8775321", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C04|rtindex:TTATCCGGAT|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C04|rtindex:TTATCCGGAT|genotype:UAS replicate1", "GSM8775321", "GSM8775321: Well P1 04C; Danio rerio; OTHER", "GSM8775321 r1", "GSM8775321", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04C.R1.fastq.gz P1-04C.R2.fastq.gz P1-04C_S27_I1_001.fastq.gz", "fastq fastq fastq", 41102932.0, 446771.0, "GSM8775321 r1", "0:34 1:48 2:10", "A:7556055;C:2874427;G:6121487;T:4864586;N:28453", 34, 48, 10, null, 7556055, 2874427, 6121487, 4864586, 28453, "SRX27572996", "SRS23984650", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34741, "SRR32232953", "SRX27572995", "SRS23984648", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04B", "GSM8775320", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 B04|rtindex:ACTCAATAGG|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04B", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 B04|rtindex:ACTCAATAGG|genotype:UAS replicate1", "GSM8775320", "GSM8775320: Well P1 04B; Danio rerio; OTHER", "GSM8775320 r1", "GSM8775320", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04B.R1.fastq.gz P1-04B.R2.fastq.gz P1-04B_S26_I1_001.fastq.gz", "fastq fastq fastq", 39908772.0, 433791.0, "GSM8775320 r1", "0:34 1:48 2:10", "A:7097865;C:2701376;G:6191071;T:4805009;N:26647", 34, 48, 10, null, 7097865, 2701376, 6191071, 4805009, 26647, "SRX27572995", "SRS23984648", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34742, "SRR32232954", "SRX27572994", "SRS23984647", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 04A", "GSM8775319", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 A04|rtindex:CTGATGGTCA|genotype:UAS replicate1|geo loc name:missing|collection date:missing", "Well P1 04A", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 A04|rtindex:CTGATGGTCA|genotype:UAS replicate1", "GSM8775319", "GSM8775319: Well P1 04A; Danio rerio; OTHER", "GSM8775319 r1", "GSM8775319", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-04A.R1.fastq.gz P1-04A.R2.fastq.gz P1-04A_S25_I1_001.fastq.gz", "fastq fastq fastq", 74926548.0, 814419.0, "GSM8775319 r1", "0:34 1:48 2:10", "A:14546606;C:5316463;G:9739043;T:9434376;N:55624", 34, 48, 10, null, 14546606, 5316463, 9739043, 9434376, 55624, "SRX27572994", "SRS23984647", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34743, "SRR32232955", "SRX27572993", "SRS23984646", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 11A", "GSM8775374", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 A11|rtindex:AATTAAGACT|genotype:GAL4UAS replicate3|geo loc name:missing|collection date:missing", "Well P1 11A", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 A11|rtindex:AATTAAGACT|genotype:GAL4UAS replicate3", "GSM8775374", "GSM8775374: Well P1 11A; Danio rerio; OTHER", "GSM8775374 r1", "GSM8775374", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-11A.R1.fastq.gz P1-11A.R2.fastq.gz P1-11A_S81_I1_001.fastq.gz", "fastq fastq fastq", 23002760.0, 250030.0, "GSM8775374 r1", "0:34 1:48 2:10", "A:3455540;C:1563605;G:4264428;T:2701802;N:16065", 34, 48, 10, null, 3455540, 1563605, 4264428, 2701802, 16065, "SRX27572993", "SRS23984646", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34744, "SRR32232956", "SRX27572992", "SRS23984645", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10G", "GSM8775373", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G10|rtindex:ATCCATGACT|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G10|rtindex:ATCCATGACT|genotype:wt replicate3", "GSM8775373", "GSM8775373: Well P1 10G; Danio rerio; OTHER", "GSM8775373 r1", "GSM8775373", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10G.R1.fastq.gz P1-10G.R2.fastq.gz P1-10G_S79_I1_001.fastq.gz", "fastq fastq fastq", 7274440.0, 79070.0, "GSM8775373 r1", "0:34 1:48 2:10", "A:1025995;C:453768;G:1424925;T:885556;N:5116", 34, 48, 10, null, 1025995, 453768, 1424925, 885556, 5116, "SRX27572992", "SRS23984645", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34745, "SRR32232957", "SRX27572991", "SRS23984644", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10F", "GSM8775372", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F10|rtindex:GCTGGAACTT|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F10|rtindex:GCTGGAACTT|genotype:wt replicate3", "GSM8775372", "GSM8775372: Well P1 10F; Danio rerio; OTHER", "GSM8775372 r1", "GSM8775372", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10F.R1.fastq.gz P1-10F.R2.fastq.gz P1-10F_S78_I1_001.fastq.gz", "fastq fastq fastq", 32953020.0, 358185.0, "GSM8775372 r1", "0:34 1:48 2:10", "A:5148026;C:2283765;G:5798660;T:3938086;N:24343", 34, 48, 10, null, 5148026, 2283765, 5798660, 3938086, 24343, "SRX27572991", "SRS23984644", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34746, "SRR32232958", "SRX27572990", "SRS23984643", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10E", "GSM8775371", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E10|rtindex:TATATACTAA|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E10|rtindex:TATATACTAA|genotype:wt replicate3", "GSM8775371", "GSM8775371: Well P1 10E; Danio rerio; OTHER", "GSM8775371 r1", "GSM8775371", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10E.R1.fastq.gz P1-10E.R2.fastq.gz P1-10E_S77_I1_001.fastq.gz", "fastq fastq fastq", 7366056084.0, 80065827.0, "GSM8775371 r1", "0:34 1:48 2:10", "A:1137867832;C:775309617;G:881567529;T:1042828519;N:5586199", 34, 48, 10, null, 1137867832, 775309617, 881567529, 1042828519, 5586199, "SRX27572990", "SRS23984643", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34747, "SRR32232959", "SRX27572989", "SRS23984642", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10D", "GSM8775370", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D10|rtindex:ACCGCCAACC|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D10|rtindex:ACCGCCAACC|genotype:wt replicate3", "GSM8775370", "GSM8775370: Well P1 10D; Danio rerio; OTHER", "GSM8775370 r1", "GSM8775370", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10D.R1.fastq.gz P1-10D.R2.fastq.gz P1-10D_S76_I1_001.fastq.gz", "fastq fastq fastq", 32482532.0, 353071.0, "GSM8775370 r1", "0:34 1:48 2:10", "A:4191254;C:2035744;G:6991172;T:3707782;N:21456", 34, 48, 10, null, 4191254, 2035744, 6991172, 3707782, 21456, "SRX27572989", "SRS23984642", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34748, "SRR32232960", "SRX27572988", "SRS23984641", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10C", "GSM8775369", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C10|rtindex:ACTTAACCTT|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C10|rtindex:ACTTAACCTT|genotype:wt replicate3", "GSM8775369", "GSM8775369: Well P1 10C; Danio rerio; OTHER", "GSM8775369 r1", "GSM8775369", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10C.R1.fastq.gz P1-10C.R2.fastq.gz P1-10C_S75_I1_001.fastq.gz", "fastq fastq fastq", 29742312.0, 323286.0, "GSM8775369 r1", "0:34 1:48 2:10", "A:4641549;C:2072399;G:5265185;T:3517381;N:21214", 34, 48, 10, null, 4641549, 2072399, 5265185, 3517381, 21214, "SRX27572988", "SRS23984641", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34749, "SRR32232961", "SRX27572987", "SRS23984640", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10B", "GSM8775368", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 B10|rtindex:TTACCGAGGC|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10B", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 B10|rtindex:TTACCGAGGC|genotype:wt replicate3", "GSM8775368", "GSM8775368: Well P1 10B; Danio rerio; OTHER", "GSM8775368 r1", "GSM8775368", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10B.R1.fastq.gz P1-10B.R2.fastq.gz P1-10B_S74_I1_001.fastq.gz", "fastq fastq fastq", 23657432.0, 257146.0, "GSM8775368 r1", "0:34 1:48 2:10", "A:3666551;C:1613324;G:4291430;T:2755799;N:15904", 34, 48, 10, null, 3666551, 1613324, 4291430, 2755799, 15904, "SRX27572987", "SRS23984640", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34750, "SRR32232962", "SRX27572986", "SRS23984639", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 10A", "GSM8775367", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 A10|rtindex:TAGATCTACT|genotype:wt replicate3|geo loc name:missing|collection date:missing", "Well P1 10A", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 A10|rtindex:TAGATCTACT|genotype:wt replicate3", "GSM8775367", "GSM8775367: Well P1 10A; Danio rerio; OTHER", "GSM8775367 r1", "GSM8775367", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-10A.R1.fastq.gz P1-10A.R2.fastq.gz P1-10A_S73_I1_001.fastq.gz", "fastq fastq fastq", 20690064.0, 224892.0, "GSM8775367 r1", "0:34 1:48 2:10", "A:3162846;C:1394801;G:3805546;T:2416575;N:15048", 34, 48, 10, null, 3162846, 1394801, 3805546, 2416575, 15048, "SRX27572986", "SRS23984639", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34751, "SRR32232963", "SRX27572985", "SRS23984638", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06H", "GSM8775342", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 H06|rtindex:AGAGCCAAGG|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06H", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 H06|rtindex:AGAGCCAAGG|genotype:wt replicate2", "GSM8775342", "GSM8775342: Well P1 06H; Danio rerio; OTHER", "GSM8775342 r1", "GSM8775342", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06H.R1.fastq.gz P1-06H.R2.fastq.gz P1-06H_S48_I1_001.fastq.gz", "fastq fastq fastq", 63664.0, 692.0, "GSM8775342 r1", "0:34 1:48 2:10", "A:13330;C:4382;G:7530;T:7889;N:85", 34, 48, 10, null, 13330, 4382, 7530, 7889, 85, "SRX27572985", "SRS23984638", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34752, "SRR32232964", "SRX27572984", "SRS23984637", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06G", "GSM8775341", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 G06|rtindex:GGAGGATAGC|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06G", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 G06|rtindex:GGAGGATAGC|genotype:wt replicate2", "GSM8775341", "GSM8775341: Well P1 06G; Danio rerio; OTHER", "GSM8775341 r1", "GSM8775341", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06G.R1.fastq.gz P1-06G.R2.fastq.gz P1-06G_S47_I1_001.fastq.gz", "fastq fastq fastq", 35465816.0, 385498.0, "GSM8775341 r1", "0:34 1:48 2:10", "A:5266761;C:2313383;G:6547005;T:4353297;N:23458", 34, 48, 10, null, 5266761, 2313383, 6547005, 4353297, 23458, "SRX27572984", "SRS23984637", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34753, "SRR32232965", "SRX27572983", "SRS23984636", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06F", "GSM8775340", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 F06|rtindex:TCAACGTAAG|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06F", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 F06|rtindex:TCAACGTAAG|genotype:wt replicate2", "GSM8775340", "GSM8775340: Well P1 06F; Danio rerio; OTHER", "GSM8775340 r1", "GSM8775340", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06F.R1.fastq.gz P1-06F.R2.fastq.gz P1-06F_S46_I1_001.fastq.gz", "fastq fastq fastq", 40023036.0, 435033.0, "GSM8775340 r1", "0:34 1:48 2:10", "A:6489618;C:2824422;G:6833067;T:4706650;N:27827", 34, 48, 10, null, 6489618, 2824422, 6833067, 4706650, 27827, "SRX27572983", "SRS23984636", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34754, "SRR32232966", "SRX27572982", "SRS23984635", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06E", "GSM8775339", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 E06|rtindex:ACGCGAGATT|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06E", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 E06|rtindex:ACGCGAGATT|genotype:wt replicate2", "GSM8775339", "GSM8775339: Well P1 06E; Danio rerio; OTHER", "GSM8775339 r1", "GSM8775339", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06E.R1.fastq.gz P1-06E.R2.fastq.gz P1-06E_S45_I1_001.fastq.gz", "fastq fastq fastq", 59610020.0, 647935.0, "GSM8775339 r1", "0:34 1:48 2:10", "A:10804415;C:4165808;G:9006405;T:7083045;N:41207", 34, 48, 10, null, 10804415, 4165808, 9006405, 7083045, 41207, "SRX27572982", "SRS23984635", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34755, "SRR32232967", "SRX27572981", "SRS23984633", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06D", "GSM8775338", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 D06|rtindex:CATACTCCGA|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06D", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 D06|rtindex:CATACTCCGA|genotype:wt replicate2", "GSM8775338", "GSM8775338: Well P1 06D; Danio rerio; OTHER", "GSM8775338 r1", "GSM8775338", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06D.R1.fastq.gz P1-06D.R2.fastq.gz P1-06D_S44_I1_001.fastq.gz", "fastq fastq fastq", 4944350388.0, 53742939.0, "GSM8775338 r1", "0:34 1:48 2:10", "A:924216784;C:417859577;G:514301359;T:719732920;N:3550432", 34, 48, 10, null, 924216784, 417859577, 514301359, 719732920, 3550432, "SRX27572981", "SRS23984633", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"], [34756, "SRR32232968", "SRX27572980", "SRS23984634", "SRP561592", "PRJNA1219235", "Neurobehavioral phenotypes in the pan neuronal GAL4 zebrafish line Tgelavl3:KalTA4", "GSE288775", "Transcriptome Analysis", "The Gal4/UAS system is used across model organisms to overexpress target genes in precise cell types and relies on generating transgenic Gal4 driver lines. In zebrafish  the Tgelavl3:KalTA4 HuC line drives robust expression in neurons. We observed an increased prevalence of swim bladder defects in Tgelavl3:KalTA4 zebrafish larvae compared to wildtype siblings  which prompted us to investigate whether transgenic larvae display additional neurobehavioral phenotypes. Tgelavl3:KalTA4 larvae showed alterations in brain activity  brain morphology  and behavior  including increased hindbrain size and reduced activity of the cerebellum. Bulk RNA seq analysis revealed massive dysregulation of the transcriptome and suggested an increased ratio of neuronal progenitor cells compared to differentiated neurons. To understand whether these phenotypes derive from Gal4 toxicity or from positional effects related to transgenesis  we used economical low pass whole genome sequencing to map the Tol2 mediated insertion site to chromosome eight. Reduced expression of the neighboring gene gadd45ga  a known cell cycle regulator  is consistent with increased proliferation and suggests a role for positional effects. Challenges with creating alternative pan neuronal lines include the length of the elavl3 HuC promoter 9 kb and random insertion using traditional transgenesis methods. To facilitate the generation of alternative lines  we cloned five neuronal promoters atp6v0cb  elavl3  rtn1a  sncb  and stmn1b ranging from 1.7 kb to 4.3 kb and created KalTA4 lines using Tol2 and the phiC31 integrase based pIGLET system. Our study highlights the importance of using appropriate genetic controls and establishes a roadmap for identifying positional effects in new transgenic lines. Overall design: Tgelavl3:KalTA4 zebrafish were crossed with Tg4xUAS hmgn6 zebrafish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  heads were collected for sci RNA seq.", null, null, null, "Well P1 06C", "GSM8775337", null, "source name:6 dpf head|tissue:6 dpf head|well:P1 C06|rtindex:GCAGGTCCGT|genotype:wt replicate2|geo loc name:missing|collection date:missing", "Well P1 06C", "Demultiplexing  trimming  alignment  filtering  and gene count processing were performed on the UMass Chan High Performance Computing cluster using scripts available from https://github.com/bethmartin/sci RNA seq3 pipeline/tree/master. Reads were aligned to GRCz11 release 104 using the Zebrafish Transcriptome Annotation version 4.3.2 Lawson et al. 2020. Assembly: GRCz11 Supplementary files format and content: RDS containing Seurat object with cell level features  counts  and barcodes Library strategy: sci RNA seq", "6 dpf head", null, "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", "Sci RNA seq was conducted following the \u201cTiny Sci\u201d protocol Martin et al. 2023. Briefly  Tgelavl3:KalTA4 fish were crossed with Tg4xUAS hmgn6 fish to produce wildtype  elavl3:KalTA4  4xUAS hmgn6  and elavl3:KalTA4; 4xUAS hmgn6 offspring. At 6 dpf  larvae were anesthetized with MS 222 and heads were removed and frozen on dry ice. The remaining body was saved for genotyping.", "tissue:6 dpf head|well:P1 C06|rtindex:GCAGGTCCGT|genotype:wt replicate2", "GSM8775337", "GSM8775337: Well P1 06C; Danio rerio; OTHER", "GSM8775337 r1", "GSM8775337", "1", "tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 \u00b5l lysis buffer B in DNA LowBind tubes Eppendorf  002431021. Heads were homogenized with a tissue homogenizer at 1 second intervals for 30 45 seconds until no clumps remained. Following fixation with ice cold methanol and dithiobis succinimidyl propionate DSP  Thermo Fisher  22586  nuclei were resuspended in sucrose PBS TritonX MgCl2 SPBSTM and sonicated for 12 seconds on low at 4\u00b0C using a Bioruptor\u00ae Pico Diagenode. Nuclei were resuspended in SPBSTM with dNTPs  and 5 ul of each of the twelve samples was pipetted into each well of one column of a twin.tec LoBind PCR plate Eppendorf  0030129512. Reverse transcription  ligation  final distribution  second strand synthesis  protease digestion  tagmentation  PCR amplification  and purification were performed as described except that tagmentation was 10 minutes instead of 5 minutes Martin et al. 2023. Approximately 1000 nuclei were added to each well during the final distribution step. Plate 1 primer sequences were used for reverse transcription  ligation  and PCR. The library was sequenced on a NextSeq500 by the UAB Heflin Center for Genomic Science Core Laboratories using a 75 cycle kit and 34 cycles for Read1  10 cycles for Index  and 48 cycles for Read2.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP561592", null, "loader:fastq load.py", "P1-06C.R1.fastq.gz P1-06C.R2.fastq.gz P1-06C_S43_I1_001.fastq.gz", "fastq fastq fastq", 37857448.0, 411494.0, "GSM8775337 r1", "0:34 1:48 2:10", "A:6636308;C:2636497;G:5984141;T:4469989;N:24777", 34, 48, 10, null, 6636308, 2636497, 5984141, 4469989, 24777, "SRX27572980", "SRS23984634", "SRA2070568", "UMass Chan", "UMass Chan", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2025-02-04", "Larval", "Larval", "Head", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 237, 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