{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation = \"Head\"", "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"], [8059, "ERR022480", "ERX008923", "ERS000088", "ERP000400", "PRJEB2333", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E-MTAB-434", "Other", null, null, null, null, "ZF female head sample1", "SAMEA708836", "Wellcome Sanger Institute", "Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio", null, null, null, null, null, null, null, null, "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E MTAB 434:sequencing of Zebrafish adult female head", "RNA from Zebrafish adult female head", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.", "Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head", "FL-cDNA", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP000400", "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16", "2719_5.srf", "srf", 1622590272.0, 15023984.0, "E MTAB 434:2719 5.srf", "0:54 1:54", "A:426435544;C:373743071;G:387589492;T:432086510;N:2735655", 54, 54, null, null, 426435544, 373743071, 387589492, 432086510, 2735655, "ERX008923", "ERS000088", "ERA015179", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.94624, 0.94338, 0.17949, 0.17965, 0.66454, 0.66872, 0.51097, 0.51377, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2010-02-26", "Adult", "Adult", "Head", "Nervous System"], [8060, "ERR022481", "ERX008923", "ERS000088", "ERP000400", "PRJEB2333", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E-MTAB-434", "Other", null, null, null, null, "ZF female head sample1", "SAMEA708836", "Wellcome Sanger Institute", "Alias:ZF female head sample1|Description:RNA extracted from female adult zebrafish head|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:24:37Z|INSDC status:public|SRA accession:ERS000088|Sample Name:ERS000088|Sex:female|Strain:Tuebingen|Title:Danio rerio", null, null, null, null, null, null, null, null, "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "E MTAB 434:sequencing of Zebrafish adult female head", "RNA from Zebrafish adult female head", "Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C.   Collected samples were snap frozen on dry ice and stored at  70 C. Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 150 to 200 bp.", "Experimental Factor: DEVELPOMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head", "FL-cDNA", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer II", null, "ERP000400", "Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer", "ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16", "2719_6.srf", "srf", 1693460736.0, 15680192.0, "E MTAB 434:2719 6.srf", "0:54 1:54", "A:445666325;C:389360280;G:403789644;T:451529226;N:3115261", 54, 54, null, null, 445666325, 389360280, 403789644, 451529226, 3115261, "ERX008923", "ERS000088", "ERA015179", "SC|Wellcome Trust Sanger Institute", "SC|Wellcome Trust Sanger Institute", 2, 0.94579, 0.94429, 0.17895, 0.17923, 0.66864, 0.67164, 0.51788, 0.51083, 54, 54, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2010-02-26", "Adult", "Adult", "Head", "Nervous System"], [11025, "ERR9787516", "ERX9334792", "ERS12088364", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 9", "SAMEA14460887", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460887|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:24Z|INSDC last update:2022 09 12T12:19:24Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 9|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 9|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 9 p", "Sample 9 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "TSCHOM1_1.fastq.gz TSCHOM1_2.fastq.gz", "fastq fastq", 6360351174.0, 31486887.0, "E MTAB 11776:TSCHOM1 ", "0:101 1:101", "A:1750731340;C:1410426576;G:1460021447;T:1739131898;N:39913", 101, 101, null, null, 1750731340, 1410426576, 1460021447, 1739131898, 39913, "ERX9334792", "ERS12088364", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93517, 0.92417, 0.15551, 0.15199, 0.67736, 0.6786, 0.48763, 0.48988, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11026, "ERR9787515", "ERX9334791", "ERS12088363", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 8", "SAMEA14460886", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460886|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:24Z|INSDC last update:2022 09 12T12:19:24Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 8|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 8|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 8 p", "Sample 8 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "DEPHOM4_1.fastq.gz DEPHOM4_2.fastq.gz", "fastq fastq", 6195443828.0, 30670514.0, "E MTAB 11776:DEPHOM4 ", "0:101 1:101", "A:1524344281;C:1573560980;G:1585093004;T:1512406843;N:38720", 101, 101, null, null, 1524344281, 1573560980, 1585093004, 1512406843, 38720, "ERX9334791", "ERS12088363", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.95088, 0.9542, 0.17631, 0.17203, 0.71121, 0.70981, 0.56015, 0.57999, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11027, "ERR9787514", "ERX9334790", "ERS12088362", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 7", "SAMEA14460885", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460885|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 7|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 7|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 7 p", "Sample 7 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "DEPHOM7_1.fastq.gz DEPHOM7_2.fastq.gz", "fastq fastq", 6201660378.0, 30701289.0, "E MTAB 11776:DEPHOM7 ", "0:101 1:101", "A:1699906420;C:1382805098;G:1427335171;T:1691574092;N:39597", 101, 101, null, null, 1699906420, 1382805098, 1427335171, 1691574092, 39597, "ERX9334790", "ERS12088362", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.92781, 0.92603, 0.15556, 0.15416, 0.67965, 0.67963, 0.48209, 0.48229, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11028, "ERR9787513", "ERX9334789", "ERS12088361", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 6", "SAMEA14460884", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460884|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 6|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 6|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 6 p", "Sample 6 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "DEPHOM6_1.fastq.gz DEPHOM6_2.fastq.gz", "fastq fastq", 6255857382.0, 30969591.0, "E MTAB 11776:DEPHOM6 ", "0:101 1:101", "A:1722554517;C:1398134491;G:1424183345;T:1710945949;N:39080", 101, 101, null, null, 1722554517, 1398134491, 1424183345, 1710945949, 39080, "ERX9334789", "ERS12088361", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93476, 0.93206, 0.16121, 0.1592, 0.67882, 0.67898, 0.48043, 0.47851, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11029, "ERR9787512", "ERX9334788", "ERS12088360", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 5", "SAMEA14460883", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460883|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 5|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 5|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 5 p", "Sample 5 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "DEPHOM1_1.fastq.gz DEPHOM1_2.fastq.gz", "fastq fastq", 6340417006.0, 31388203.0, "E MTAB 11776:DEPHOM1 ", "0:101 1:101", "A:1738622221;C:1420060351;G:1455477148;T:1726216833;N:40453", 101, 101, null, null, 1738622221, 1420060351, 1455477148, 1726216833, 40453, "ERX9334788", "ERS12088360", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93634, 0.93167, 0.15036, 0.14813, 0.67809, 0.67813, 0.47978, 0.47851, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11030, "ERR9787511", "ERX9334787", "ERS12088359", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 4", "SAMEA14460882", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460882|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 4|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 /  x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 4|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 4 p", "Sample 4 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 /  x tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "2XHOM7_1.fastq.gz 2XHOM7_2.fastq.gz", "fastq fastq", 6291880446.0, 31147923.0, "E MTAB 11776:2XHOM7 ", "0:101 1:101", "A:1712784902;C:1424143534;G:1452943449;T:1701969086;N:39475", 101, 101, null, null, 1712784902, 1424143534, 1452943449, 1701969086, 39475, "ERX9334787", "ERS12088359", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93869, 0.93511, 0.15405, 0.15042, 0.67377, 0.67351, 0.50599, 0.50683, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11031, "ERR9787510", "ERX9334786", "ERS12088358", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 3", "SAMEA14460881", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460881|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 /  x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 3|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 3 p", "Sample 3 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 /  x tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "2XHOM6_1.fastq.gz 2XHOM6_2.fastq.gz", "fastq fastq", 6214327596.0, 30763998.0, "E MTAB 11776:2XHOM6 ", "0:101 1:101", "A:1705019759;C:1384064144;G:1432455427;T:1692749964;N:38302", 101, 101, null, null, 1705019759, 1384064144, 1432455427, 1692749964, 38302, "ERX9334786", "ERS12088358", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93591, 0.92636, 0.14492, 0.14145, 0.67489, 0.67491, 0.47753, 0.49286, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11032, "ERR9787509", "ERX9334785", "ERS12088357", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 2", "SAMEA14460880", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460880|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 /  x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 2|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 2 p", "Sample 2 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 /  x tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "2XHOM4_1.fastq.gz 2XHOM4_2.fastq.gz", "fastq fastq", 6301691990.0, 31196495.0, "E MTAB 11776:2XHOM4 ", "0:101 1:101", "A:1698118705;C:1442276237;G:1473988715;T:1687268823;N:39510", 101, 101, null, null, 1698118705, 1442276237, 1473988715, 1687268823, 39510, "ERX9334785", "ERS12088357", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.94255, 0.93839, 0.13232, 0.13007, 0.67326, 0.67294, 0.49084, 0.49291, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11033, "ERR9787508", "ERX9334784", "ERS12088356", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 16", "SAMEA14460879", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460879|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 16|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 16|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 16 p", "Sample 16 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "WT7_1.fastq.gz WT7_2.fastq.gz", "fastq fastq", 6206666746.0, 30726073.0, "E MTAB 11776:WT7 ", "0:101 1:101", "A:1705689174;C:1387290312;G:1420249657;T:1693397929;N:39674", 101, 101, null, null, 1705689174, 1387290312, 1420249657, 1693397929, 39674, "ERX9334784", "ERS12088356", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93493, 0.92964, 0.15803, 0.1554, 0.67405, 0.67501, 0.47988, 0.46768, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11034, "ERR9787507", "ERX9334783", "ERS12088355", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 15", "SAMEA14460878", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460878|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 15|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 15|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 15 p", "Sample 15 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "WT6_1.fastq.gz WT6_2.fastq.gz", "fastq fastq", 6360740630.0, 31488815.0, "E MTAB 11776:WT6 ", "0:101 1:101", "A:1735195643;C:1436805269;G:1469558083;T:1719141699;N:39936", 101, 101, null, null, 1735195643, 1436805269, 1469558083, 1719141699, 39936, "ERX9334783", "ERS12088355", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93629, 0.93343, 0.15169, 0.1501, 0.67572, 0.67517, 0.47499, 0.47879, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11035, "ERR9787506", "ERX9334782", "ERS12088354", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 14", "SAMEA14460877", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460877|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 14|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 14|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 14 p", "Sample 14 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "WT4_1.fastq.gz WT4_2.fastq.gz", "fastq fastq", 6227472342.0, 30829071.0, "E MTAB 11776:WT4 ", "0:101 1:101", "A:1668352581;C:1434152947;G:1468645621;T:1656281986;N:39207", 101, 101, null, null, 1668352581, 1434152947, 1468645621, 1656281986, 39207, "ERX9334782", "ERS12088354", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.94261, 0.93675, 0.15334, 0.15049, 0.67927, 0.67872, 0.48762, 0.49138, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11036, "ERR9787505", "ERX9334781", "ERS12088353", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 13", "SAMEA14460876", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460876|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 13|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 13|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 13 p", "Sample 13 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "WT1_1.fastq.gz WT1_2.fastq.gz", "fastq fastq", 6332757570.0, 31350285.0, "E MTAB 11776:WT1 ", "0:101 1:101", "A:1726838066;C:1431452165;G:1460746594;T:1713681043;N:39702", 101, 101, null, null, 1726838066, 1431452165, 1460746594, 1713681043, 39702, "ERX9334781", "ERS12088353", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.92422, 0.93556, 0.14884, 0.14926, 0.67694, 0.67564, 0.48223, 0.48884, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11037, "ERR9787504", "ERX9334780", "ERS12088352", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 12", "SAMEA14460875", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460875|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 12|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 12|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 12 p", "Sample 12 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "TSCHOM7_1.fastq.gz TSCHOM7_2.fastq.gz", "fastq fastq", 6216990360.0, 30777180.0, "E MTAB 11776:TSCHOM7 ", "0:101 1:101", "A:1710256020;C:1390027205;G:1419250792;T:1697417099;N:39244", 101, 101, null, null, 1710256020, 1390027205, 1419250792, 1697417099, 39244, "ERX9334780", "ERS12088352", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93162, 0.92801, 0.15191, 0.14943, 0.67789, 0.67951, 0.47915, 0.47762, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11038, "ERR9787503", "ERX9334779", "ERS12088351", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 11", "SAMEA14460874", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460874|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 11|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 11|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 11 p", "Sample 11 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "TSCHOM6_1.fastq.gz TSCHOM6_2.fastq.gz", "fastq fastq", 6199081848.0, 30688524.0, "E MTAB 11776:TSCHOM6 ", "0:101 1:101", "A:1705859045;C:1387530558;G:1415224718;T:1690428701;N:38826", 101, 101, null, null, 1705859045, 1387530558, 1415224718, 1690428701, 38826, "ERX9334779", "ERS12088351", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93583, 0.93349, 0.15923, 0.15664, 0.67976, 0.67986, 0.48632, 0.48376, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11039, "ERR9787502", "ERX9334778", "ERS12088350", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 10", "SAMEA14460873", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460873|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 10|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 10|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 10 p", "Sample 10 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "TSCHOM4_1.fastq.gz TSCHOM4_2.fastq.gz", "fastq fastq", 6287836204.0, 31127902.0, "E MTAB 11776:TSCHOM4 ", "0:101 1:101", "A:1673762523;C:1453880149;G:1493343671;T:1666809849;N:40012", 101, 101, null, null, 1673762523, 1453880149, 1493343671, 1666809849, 40012, "ERX9334778", "ERS12088350", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.94269, 0.9375, 0.14166, 0.13979, 0.67476, 0.67722, 0.4927, 0.49365, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [11040, "ERR9787501", "ERX9334777", "ERS12088349", "ERP137937", "PRJEB53153", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E-MTAB-11776", "Transcriptome Analysis", "Transcriptome analysis of the heads of 5 dpf epdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a /  zebrafish larvae.", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", null, "Protocols: 5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Sample 1", "SAMEA14460872", "Laboratory for Molecular Biodiscovery, KU Leuven", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12|External Id:SAMEA14460872|INSDC center alias:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC center name:Laboratory for Molecular Biodiscovery  KU Leuven|INSDC first public:2022 09 12T12:19:23Z|INSDC last update:2022 09 12T12:19:23Z|INSDC status:public|Submitter Id:E MTAB 11776:Sample 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:depdc5 /  x tsc2 / |individual:pool of 10 larvae|isolate:not applicable|organism part:head|sample name:E MTAB 11776:Sample 1|scientific name:Danio rerio|sex:non available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "E MTAB 11776:Sample 1 p", "Sample 1 p", "RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "5 dpf zebrafish larvae were anesthetized and decapitated using a razor blade. 10 heads were pooled in quadruplicate per genotype. otal RNA was extracted using TRIzol reagent Invitrogen  followed by phenol chlorophorm extraction and isopropanol precipitation. post ethanol washes  the RNA pellet was air dried  dissolved in nuclease free water Fermentas. Illumina TruSeq Stranded mRNA Seq sample preparation kit was used to prepare the mRNA sequencing library according to the manufacturer guidelines.", "Experimental Factor: genotype:depdc5 /  x tsc2 / ", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP137937", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of depdc5 /   tsc2 /   depdc5 /  x tsc2 /  and wildtype zebrafish larvae", "ENA FIRST PUBLIC:2022 09 12|ENA LAST UPDATE:2022 09 12", "2XHOM1_1.fastq.gz 2XHOM1_2.fastq.gz", "fastq fastq", 6232605768.0, 30854484.0, "E MTAB 11776:2XHOM1 ", "0:101 1:101", "A:1725401812;C:1384507160;G:1410306583;T:1712351429;N:38784", 101, 101, null, null, 1725401812, 1384507160, 1410306583, 1712351429, 38784, "ERX9334777", "ERS12088349", "ERA14756702", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", "Laboratory for Molecular Biodiscovery, KU Leuven|European Nucleotide Archive", 2, 0.93594, 0.93262, 0.15282, 0.14977, 0.67503, 0.67373, 0.49522, 0.49759, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Belgium", "2022-09-12", "Larval", "Larval", "Head", "Nervous System"], [32068, "SRR29007557", "SRX24534635", "SRS21280318", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Wt 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Wt 1", "Kcnd2 Wt 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Wt_1_1.fq.gz Kcnd2_Wt_1_2.fq.gz", "fastq fastq", 6772910100.0, 22576367.0, "Kcnd2 Wt 1 1.fq.gz", "0:150 1:150", "A:1933789152;C:1464135438;G:1474439143;T:1900463092;N:83275", 150, 150, null, null, 1933789152, 1464135438, 1474439143, 1900463092, 83275, "SRX24534635", "SRS21280318", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32069, "SRR29007558", "SRX24534634", "SRS21280317", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Hom 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Hom 3", "Arfgef1 Hom 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Hom_3_1.fq.gz Arfgef1_Hom_3_2.fq.gz", "fastq fastq", 7294731000.0, 24315770.0, "Arfgef1 Hom 3 1.fq.gz", "0:150 1:150", "A:1847018467;C:1809604703;G:1818278888;T:1819707786;N:121156", 150, 150, null, null, 1847018467, 1809604703, 1818278888, 1819707786, 121156, "SRX24534634", "SRS21280317", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32070, "SRR29007559", "SRX24534633", "SRS21280316", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Hom 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Hom 2", "Arfgef1 Hom 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Hom_2_1.fq.gz Arfgef1_Hom_2_2.fq.gz", "fastq fastq", 6607825200.0, 22026084.0, "Arfgef1 Hom 2 1.fq.gz", "0:150 1:150", "A:1694417387;C:1616938849;G:1625276704;T:1671046414;N:145846", 150, 150, null, null, 1694417387, 1616938849, 1625276704, 1671046414, 145846, "SRX24534633", "SRS21280316", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32071, "SRR29007560", "SRX24534632", "SRS21280315", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Hom 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Hom1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Hom 1", "Arfgef1 Hom 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Hom_1_1.fq.gz Arfgef1_Hom_1_2.fq.gz", "fastq fastq", 6777738600.0, 22592462.0, "Arfgef1 Hom 1 1.fq.gz", "0:150 1:150", "A:1739306802;C:1658195023;G:1665806667;T:1714318423;N:111685", 150, 150, null, null, 1739306802, 1658195023, 1665806667, 1714318423, 111685, "SRX24534632", "SRS21280315", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32072, "SRR29007561", "SRX24534631", "SRS21280314", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Het 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Het 3", "Arfgef1 Het 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Het_3_1.fq.gz Arfgef1_Het_3_2.fq.gz", "fastq fastq", 6739993500.0, 22466645.0, "Arfgef1 Het 3 1.fq.gz", "0:150 1:150", "A:1725253563;C:1652471358;G:1662793828;T:1699392429;N:82322", 150, 150, null, null, 1725253563, 1652471358, 1662793828, 1699392429, 82322, "SRX24534631", "SRS21280314", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32073, "SRR29007562", "SRX24534630", "SRS21280313", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Het 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Het 2", "Arfgef1 Het 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Het_2_1.fq.gz Arfgef1_Het_2_2.fq.gz", "fastq fastq", 9510813000.0, 31702710.0, "Arfgef1 Het 2 1.fq.gz", "0:150 1:150", "A:2509621883;C:2259671963;G:2271899998;T:2469380560;N:238596", 150, 150, null, null, 2509621883, 2259671963, 2271899998, 2469380560, 238596, "SRX24534630", "SRS21280313", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32074, "SRR29007563", "SRX24534629", "SRS21280312", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Het 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Het1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Het 1", "Arfgef1 Het 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Het_1_1.fq.gz Arfgef1_Het_1_2.fq.gz", "fastq fastq", 6887369100.0, 22957897.0, "Arfgef1 Het 1 1.fq.gz", "0:150 1:150", "A:1766549896;C:1685533018;G:1694949682;T:1740214059;N:122445", 150, 150, null, null, 1766549896, 1685533018, 1694949682, 1740214059, 122445, "SRX24534629", "SRS21280312", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32075, "SRR29007564", "SRX24534628", "SRS21280311", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Hom 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Hom 3", "Wnt8b Hom 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Hom_3_1.fq.gz Wnt8b_Hom_3_2.fq.gz", "fastq fastq", 10567857900.0, 35226193.0, "Wnt8b Hom 3 1.fq.gz", "0:150 1:150", "A:2775044850;C:2525957688;G:2527072827;T:2739479844;N:302691", 150, 150, null, null, 2775044850, 2525957688, 2527072827, 2739479844, 302691, "SRX24534628", "SRS21280311", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32076, "SRR29007565", "SRX24534627", "SRS21280310", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Hom 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Hom 2", "Wnt8b Hom 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Hom_2_1.fq.gz Wnt8b_Hom_2_2.fq.gz", "fastq fastq", 7666806600.0, 25556022.0, "Wnt8b Hom 2 1.fq.gz", "0:150 1:150", "A:2029345938;C:1820579149;G:1819606043;T:1996786660;N:488810", 150, 150, null, null, 2029345938, 1820579149, 1819606043, 1996786660, 488810, "SRX24534627", "SRS21280310", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32077, "SRR29007566", "SRX24534626", "SRS21280309", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Hom 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Hom 1", "Wnt8b Hom 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Hom_1_1.fq.gz Wnt8b_Hom_1_2.fq.gz", "fastq fastq", 6514544400.0, 21715148.0, "Wnt8b Hom 1 1.fq.gz", "0:150 1:150", "A:1711943699;C:1556010812;G:1555687818;T:1690731439;N:170632", 150, 150, null, null, 1711943699, 1556010812, 1555687818, 1690731439, 170632, "SRX24534626", "SRS21280309", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32078, "SRR29007567", "SRX24534625", "SRS21280308", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Het 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Het 3", "Wnt8b Het 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Het_3_1.fq.gz Wnt8b_Het_3_2.fq.gz", "fastq fastq", 8714661900.0, 29048873.0, "Wnt8b Het 3 1.fq.gz", "0:150 1:150", "A:2360994905;C:2008091028;G:2013456743;T:2332006781;N:112443", 150, 150, null, null, 2360994905, 2008091028, 2013456743, 2332006781, 112443, "SRX24534625", "SRS21280308", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32079, "SRR29007568", "SRX24534624", "SRS21280307", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Het 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Het 2", "Wnt8b Het 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Het_2_1.fq.gz Wnt8b_Het_2_2.fq.gz", "fastq fastq", 8370112800.0, 27900376.0, "Wnt8b Het 2 1.fq.gz", "0:150 1:150", "A:2275496039;C:1920819728;G:1927597917;T:2246091711;N:107405", 150, 150, null, null, 2275496039, 1920819728, 1927597917, 2246091711, 107405, "SRX24534624", "SRS21280307", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32080, "SRR29007569", "SRX24534623", "SRS21280306", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Het 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Het1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Het 1", "Wnt8b Het 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Het_1_1.fq.gz Wnt8b_Het_1_2.fq.gz", "fastq fastq", 7614189000.0, 25380630.0, "Wnt8b Het 1 1.fq.gz", "0:150 1:150", "A:2059784093;C:1755740426;G:1761242316;T:2037325656;N:96509", 150, 150, null, null, 2059784093, 1755740426, 1761242316, 2037325656, 96509, "SRX24534623", "SRS21280306", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32081, "SRR29007570", "SRX24534622", "SRS21280305", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Wt 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Wt 3", "Wnt8b Wt 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Wt_3_1.fq.gz Wnt8b_Wt_3_2.fq.gz", "fastq fastq", 6809737500.0, 22699125.0, "Wnt8b Wt 3 1.fq.gz", "0:150 1:150", "A:1869159615;C:1548130956;G:1547169482;T:1845192460;N:84987", 150, 150, null, null, 1869159615, 1548130956, 1547169482, 1845192460, 84987, "SRX24534622", "SRS21280305", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32082, "SRR29007571", "SRX24534621", "SRS21280304", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Wt 3", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Wt 3", "Arfgef1 Wt 3", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Wt_3_1.fq.gz Arfgef1_Wt_3_2.fq.gz", "fastq fastq", 6162364200.0, 20541214.0, "Arfgef1 Wt 3 1.fq.gz", "0:150 1:150", "A:1606427072;C:1484826935;G:1488745137;T:1582299135;N:65921", 150, 150, null, null, 1606427072, 1484826935, 1488745137, 1582299135, 65921, "SRX24534621", "SRS21280304", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32083, "SRR29007572", "SRX24534620", "SRS21280303", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Wt 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Wt 2", "Wnt8b Wt 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Wt_2_1.fq.gz Wnt8b_Wt_2_2.fq.gz", "fastq fastq", 6743670600.0, 22478902.0, "Wnt8b Wt 2 1.fq.gz", "0:150 1:150", "A:1852520280;C:1531023930;G:1536795067;T:1823243896;N:87427", 150, 150, null, null, 1852520280, 1531023930, 1536795067, 1823243896, 87427, "SRX24534620", "SRS21280303", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32084, "SRR29007573", "SRX24534619", "SRS21280302", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Wt 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Wt 1", "Wnt8b Wt 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Wt_1_1.fq.gz Wnt8b_Wt_1_2.fq.gz", "fastq fastq", 6534620400.0, 21782068.0, "Wnt8b Wt 1 1.fq.gz", "0:150 1:150", "A:1783250074;C:1493088330;G:1497228073;T:1760957638;N:96285", 150, 150, null, null, 1783250074, 1493088330, 1497228073, 1760957638, 96285, "SRX24534619", "SRS21280302", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32085, "SRR29007574", "SRX24534618", "SRS21280301", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Hom 4", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Hom 4", "Kcnd2 Hom 4", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Hom_4_1.fq.gz Kcnd2_Hom_4_2.fq.gz", "fastq fastq", 7596974100.0, 25323247.0, "Kcnd2 Hom 4 1.fq.gz", "0:150 1:150", "A:2007694949;C:1807188755;G:1800403701;T:1981369650;N:317045", 150, 150, null, null, 2007694949, 1807188755, 1800403701, 1981369650, 317045, "SRX24534618", "SRS21280301", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32086, "SRR29007575", "SRX24534617", "SRS21280300", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Hom 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Hom 2", "Kcnd2 Hom 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Hom_2_1.fq.gz Kcnd2_Hom_2_2.fq.gz", "fastq fastq", 7289261100.0, 24297537.0, "Kcnd2 Hom 2 1.fq.gz", "0:150 1:150", "A:2078143741;C:1581832453;G:1587225393;T:2041970189;N:89324", 150, 150, null, null, 2078143741, 1581832453, 1587225393, 2041970189, 89324, "SRX24534617", "SRS21280300", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32087, "SRR29007576", "SRX24534616", "SRS21280299", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Hom 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Hom1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Hom 1", "Kcnd2 Hom 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Hom_1_1.fq.gz Kcnd2_Hom_1_2.fq.gz", "fastq fastq", 8331212400.0, 27770708.0, "Kcnd2 Hom 1 1.fq.gz", "0:150 1:150", "A:2185320924;C:1987553985;G:1999101969;T:2159195984;N:39538", 150, 150, null, null, 2185320924, 1987553985, 1999101969, 2159195984, 39538, "SRX24534616", "SRS21280299", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32088, "SRR29007577", "SRX24534615", "SRS21280298", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Het 4", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Het 4", "Kcnd2 Het 4", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Het_4_1.fq.gz Kcnd2_Het_4_2.fq.gz", "fastq fastq", 10195958700.0, 33986529.0, "Kcnd2 Het 4 1.fq.gz", "0:150 1:150", "A:2675050868;C:2442920285;G:2439165482;T:2638402351;N:419714", 150, 150, null, null, 2675050868, 2442920285, 2439165482, 2638402351, 419714, "SRX24534615", "SRS21280298", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32089, "SRR29007578", "SRX24534614", "SRS21280297", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Het 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Het 2", "Kcnd2 Het 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Het_2_1.fq.gz Kcnd2_Het_2_2.fq.gz", "fastq fastq", 7549108800.0, 25163696.0, "Kcnd2 Het 2 1.fq.gz", "0:150 1:150", "A:1994641167;C:1795831385;G:1796069017;T:1962477823;N:89408", 150, 150, null, null, 1994641167, 1795831385, 1796069017, 1962477823, 89408, "SRX24534614", "SRS21280297", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32090, "SRR29007579", "SRX24534613", "SRS21280296", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Het 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Het1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Het 1", "Kcnd2 Het 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Het_1_1.fq.gz Kcnd2_Het_1_2.fq.gz", "fastq fastq", 7081857600.0, 23606192.0, "Kcnd2 Het 1 1.fq.gz", "0:150 1:150", "A:1860484446;C:1694088253;G:1695161253;T:1832038793;N:84855", 150, 150, null, null, 1860484446, 1694088253, 1695161253, 1832038793, 84855, "SRX24534613", "SRS21280296", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32091, "SRR29007580", "SRX24534612", "SRS21280295", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Wt 4", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Wt 4", "Kcnd2 Wt 4", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Wt_4_1.fq.gz Kcnd2_Wt_4_2.fq.gz", "fastq fastq", 8142446700.0, 27141489.0, "Kcnd2 Wt 4 1.fq.gz", "0:150 1:150", "A:2136890254;C:1951822302;G:1947544318;T:2105854363;N:335463", 150, 150, null, null, 2136890254, 1951822302, 1947544318, 2105854363, 335463, "SRX24534612", "SRS21280295", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32092, "SRR29007581", "SRX24534611", "SRS21280294", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Kcnd2 Wt 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Kcnd2 Wt2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Kcnd2 Wt 2", "Kcnd2 Wt 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Kcnd2_Wt_2_1.fq.gz Kcnd2_Wt_2_2.fq.gz", "fastq fastq", 6688680600.0, 22295602.0, "Kcnd2 Wt 2 1.fq.gz", "0:150 1:150", "A:1902466623;C:1451301657;G:1460696794;T:1874184765;N:30761", 150, 150, null, null, 1902466623, 1451301657, 1460696794, 1874184765, 30761, "SRX24534611", "SRS21280294", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32093, "SRR29007582", "SRX24534610", "SRS21280293", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Wt 2", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Wt 2", "Arfgef1 Wt 2", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Wt_2_1.fq.gz Arfgef1_Wt_2_2.fq.gz", "fastq fastq", 7399981500.0, 24666605.0, "Arfgef1 Wt 2 1.fq.gz", "0:150 1:150", "A:1904125951;C:1807905407;G:1812898141;T:1874904149;N:147852", 150, 150, null, null, 1904125951, 1807905407, 1812898141, 1874904149, 147852, "SRX24534610", "SRS21280293", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32094, "SRR29007583", "SRX24534609", "SRS21280292", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Arfgef1 Wt 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Arfgef1 Wt1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Arfgef1 Wt 1", "Arfgef1 Wt 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Arfgef1_Wt_1_1.fq.gz Arfgef1_Wt_1_2.fq.gz", "fastq fastq", 7542057300.0, 25140191.0, "Arfgef1 Wt 1 1.fq.gz", "0:150 1:150", "A:1927852618;C:1855757148;G:1860100302;T:1898222485;N:124747", 150, 150, null, null, 1927852618, 1855757148, 1860100302, 1898222485, 124747, "SRX24534609", "SRS21280292", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32098, "SRR29008446", "SRX24535482", "SRS21281082", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Chondrocyte head biolRep3", "GSM8264152", null, "source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Chondrocyte head biolRep3", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264152", "GSM8264152: Chondrocyte head biolRep3; Danio rerio; RNA Seq", "GSM8264152 r1", "GSM8264152", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "cartilRep3_R1.fastq.gz cartilRep3_R2.fastq.gz", "fastq fastq", 6819648393.0, 25781563.0, "GSM8264152 r1", "0:132.28 1:132.24", "A:1843991471;C:1548648708;G:1568393744;T:1858508350;N:106120", 132, 132, null, null, 1843991471, 1548648708, 1568393744, 1858508350, 106120, "SRX24535482", "SRS21281082", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32099, "SRR29008447", "SRX24535481", "SRS21281081", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Chondrocyte head biolRep2", "GSM8264151", null, "source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Chondrocyte head biolRep2", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264151", "GSM8264151: Chondrocyte head biolRep2; Danio rerio; RNA Seq", "GSM8264151 r1", "GSM8264151", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "cartilRep2_R1.fastq.gz cartilRep2_R2.fastq.gz", "fastq fastq", 6328377834.0, 23616303.0, "GSM8264151 r1", "0:134.02 1:133.95", "A:1697207927;C:1464700434;G:1476121489;T:1690068467;N:279517", 134, 133, null, null, 1697207927, 1464700434, 1476121489, 1690068467, 279517, "SRX24535481", "SRS21281081", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32100, "SRR29008448", "SRX24535480", "SRS21281080", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Chondrocyte head biolRep1", "GSM8264150", null, "source name:head|tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Chondrocyte head biolRep1", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:head chondrocyte|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264150", "GSM8264150: Chondrocyte head biolRep1; Danio rerio; RNA Seq", "GSM8264150 r1", "GSM8264150", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "cartilRep1_R1.fastq.gz cartilRep1_R2.fastq.gz", "fastq fastq", 3594349367.0, 13391209.0, "GSM8264150 r1", "0:134.24 1:134.17", "A:956150712;C:837180050;G:846748291;T:954113728;N:156586", 134, 134, null, null, 956150712, 837180050, 846748291, 954113728, 156586, "SRX24535480", "SRS21281080", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32104, "SRR29008452", "SRX24535476", "SRS21281076", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Osteoblast head biolRep3", "GSM8264146", null, "source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Osteoblast head biolRep3", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264146", "GSM8264146: Osteoblast head biolRep3; Danio rerio; RNA Seq", "GSM8264146 r1", "GSM8264146", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "osteobRep3_R1.fastq.gz osteobRep3_R2.fastq.gz", "fastq fastq", 4016101824.0, 15220140.0, "GSM8264146 r1", "0:131.95 1:131.92", "A:1091466642;C:915105554;G:923772050;T:1085593417;N:164161", 131, 131, null, null, 1091466642, 915105554, 923772050, 1085593417, 164161, "SRX24535476", "SRS21281076", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32105, "SRR29008453", "SRX24535475", "SRS21281075", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Osteoblast head biolRep2", "GSM8264145", null, "source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Osteoblast head biolRep2", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264145", "GSM8264145: Osteoblast head biolRep2; Danio rerio; RNA Seq", "GSM8264145 r1", "GSM8264145", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "osteobRep2_R1.fastq.gz osteobRep2_R2.fastq.gz", "fastq fastq", 3692172504.0, 14317610.0, "GSM8264145 r1", "0:128.95 1:128.93", "A:1007186967;C:837532125;G:846083342;T:1001209204;N:160866", 128, 128, null, null, 1007186967, 837532125, 846083342, 1001209204, 160866, "SRX24535475", "SRS21281075", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32106, "SRR29008454", "SRX24535474", "SRS21281074", "SRP507332", "PRJNA1111082", "Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA]", "GSE267333", "Transcriptome Analysis", "Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.", null, null, null, "Osteoblast head biolRep1", "GSM8264144", null, "source name:head|tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf loc name:missing|collection date:missing", "Osteoblast head biolRep1", "QC of sequences  adapter trimming and duplicate removal using fastp package with   dedup option Sequence alignment to genome using the STAR aligner samtools to sort and index aligned reads reads counted using the featureCounts command from the Subread package Assembly: danRer11 Supplementary files format and content: tab deliminated text files including raw count for each sample 7th column", "head", null, "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "tissue:head|cell type:osteoblast classical|genotype:WT; entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry|Stage:15 dpf", "GSM8264144", "GSM8264144: Osteoblast head biolRep1; Danio rerio; RNA Seq", "GSM8264144 r1", "GSM8264144", "1", "RNA was isolated using the RNeasy Plus Micro Kit QIAGEN  74034. Samples were sent to Eurofins Genomics for library preparation and paired end sequencing with the INVIEW Transcriptome Ultra Low service 2x 150. Per sample  15M reads were sequenced.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507332", null, "loader:fastq load.py", "osteobRep1_R1.fastq.gz osteobRep1_R2.fastq.gz", "fastq fastq", 8569394356.0, 28375478.0, "GSM8264144 r1", "0:151 1:151", "A:2308551585;C:1841082082;G:2161425693;T:2253505108;N:4829888", 151, 151, null, null, 2308551585, 1841082082, 2161425693, 2253505108, 4829888, "SRX24535474", "SRS21281074", "SRA1865629", "Institute for Cardiovascular Organogenesis and Regeneration", "Institute for Cardiovascular Organogenesis and Regeneration", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-05-13", "Larval", "Larval", "Head", "Nervous System"], [32806, "SRR29478752", "SRX24989905", "SRS21691708", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  scarb2a mut  rep 3", "GSM8339369", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head  scarb2a mut  rep 3", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339369", "GSM8339369: head  scarb2a mut  rep 3; Danio rerio; RNA Seq", "GSM8339369 r1", "GSM8339369", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut3_R2.fastq.gz scarb2_mut3_R1.fastq.gz", "fastq fastq", 590803877.0, 7118119.0, "GSM8339369 r1", "0:75 1:8", "A:171152826;C:118382558;G:138973475;T:162287717;N:7301", 75, 8, null, null, 171152826, 118382558, 138973475, 162287717, 7301, "SRX24989905", "SRS21691708", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86187, 0.0, 0.06751, 0.0, 0.80081, 1.0, 0.47421, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32807, "SRR29478753", "SRX24989904", "SRS21691707", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  scarb2a mut  rep 2", "GSM8339368", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head  scarb2a mut  rep 2", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339368", "GSM8339368: head  scarb2a mut  rep 2; Danio rerio; RNA Seq", "GSM8339368 r1", "GSM8339368", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut2_R2.fastq.gz scarb2_mut2_R1.fastq.gz", "fastq fastq", 560228337.0, 6749739.0, "GSM8339368 r1", "0:75 1:8", "A:161395198;C:113034644;G:131199008;T:154592664;N:6823", 75, 8, null, null, 161395198, 113034644, 131199008, 154592664, 6823, "SRX24989904", "SRS21691707", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.85633, 0.0, 0.06116, 0.0, 0.80438, 1.0, 0.47226, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32808, "SRR29478754", "SRX24989903", "SRS21691706", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  scarb2a mut  rep 1", "GSM8339367", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head  scarb2a mut  rep 1", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339367", "GSM8339367: head  scarb2a mut  rep 1; Danio rerio; RNA Seq", "GSM8339367 r1", "GSM8339367", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut1_R1.fastq.gz scarb2_mut1_R2.fastq.gz", "fastq fastq", 536045042.0, 6458374.0, "GSM8339367 r1", "0:75 1:8", "A:152863781;C:109210501;G:126922310;T:147041910;N:6540", 75, 8, null, null, 152863781, 109210501, 126922310, 147041910, 6540, "SRX24989903", "SRS21691706", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86464, 0.0, 0.06577, 0.0, 0.80359, 1.0, 0.48395, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32809, "SRR29478755", "SRX24989902", "SRS21691705", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  wt  rep 4", "GSM8339366", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head  wt  rep 4", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339366", "GSM8339366: head  wt  rep 4; Danio rerio; RNA Seq", "GSM8339366 r1", "GSM8339366", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt4_R1.fastq.gz scarb2_wt4_R2.fastq.gz", "fastq fastq", 723943430.0, 8722210.0, "GSM8339366 r1", "0:75 1:8", "A:206155698;C:145344454;G:172171717;T:200262536;N:9025", 75, 8, null, null, 206155698, 145344454, 172171717, 200262536, 9025, "SRX24989902", "SRS21691705", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86958, 0.0, 0.0737, 0.0, 0.79928, 1.0, 0.47906, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32810, "SRR29478756", "SRX24989901", "SRS21691704", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  wt  rep 3", "GSM8339365", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head  wt  rep 3", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339365", "GSM8339365: head  wt  rep 3; Danio rerio; RNA Seq", "GSM8339365 r1", "GSM8339365", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt3_R1.fastq.gz scarb2_wt3_R2.fastq.gz", "fastq fastq", 560881132.0, 6757604.0, "GSM8339365 r1", "0:75 1:8", "A:158992539;C:112696361;G:133852695;T:155332822;N:6715", 75, 8, null, null, 158992539, 112696361, 133852695, 155332822, 6715, "SRX24989901", "SRS21691704", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.8706, 0.0, 0.07425, 0.0, 0.80038, 1.0, 0.47161, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [32811, "SRR29478757", "SRX24989900", "SRS21691703", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  wt  rep 1", "GSM8339364", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:wt|geo loc name:missing|collection date:missing", "head  wt  rep 1", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:wt", "GSM8339364", "GSM8339364: head  wt  rep 1; Danio rerio; RNA Seq", "GSM8339364 r1", "GSM8339364", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_wt1_R1.fastq.gz scarb2_wt1_R2.fastq.gz", "fastq fastq", 539653799.0, 6501853.0, "GSM8339364 r1", "0:75 1:8", "A:153571518;C:110489477;G:128477853;T:147108152;N:6799", 75, 8, null, null, 153571518, 110489477, 128477853, 147108152, 6799, "SRX24989900", "SRS21691703", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.87359, 0.0, 0.07353, 0.0, 0.80184, 1.0, 0.47111, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous System"], [33619, "SRR30310487", "SRX25770932", "SRS22407035", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "DM biol rep 3", "GSM8473259", null, "source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing", "DM biol rep 3", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a / ;5b / |treatment:untreated", "GSM8473259", "GSM8473259: DM biol rep 3; Danio rerio; RNA Seq", "GSM8473259 r1", "GSM8473259", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47814-DM3_S6_R2_001.fastq.gz Li47814-DM3_S6_R1_001.fastq.gz", "fastq fastq", 4759652497.0, 39356384.0, "GSM8473259 r1", "0:60.49 1:60.44", "A:1221224093;C:1133209753;G:1144876807;T:1252303477;N:8038367", 60, 60, null, null, 1221224093, 1133209753, 1144876807, 1252303477, 8038367, "SRX25770932", "SRS22407035", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94992, 0.95405, 0.07666, 0.07486, 0.64969, 0.648, 0.47911, 0.48137, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33620, "SRR30310488", "SRX25770931", "SRS22407034", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "DM biol rep 2", "GSM8473258", null, "source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing", "DM biol rep 2", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a / ;5b / |treatment:untreated", "GSM8473258", "GSM8473258: DM biol rep 2; Danio rerio; RNA Seq", "GSM8473258 r1", "GSM8473258", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47813-DM2_S5_R2_001.fastq.gz Li47813-DM2_S5_R1_001.fastq.gz", "fastq fastq", 5030260806.0, 41607672.0, "GSM8473258 r1", "0:60.47 1:60.43", "A:1291665135;C:1198581962;G:1206075180;T:1323425262;N:10513267", 60, 60, null, null, 1291665135, 1198581962, 1206075180, 1323425262, 10513267, "SRX25770931", "SRS22407034", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94958, 0.95221, 0.08402, 0.0824, 0.64628, 0.64553, 0.47628, 0.47968, 61, 60, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33621, "SRR30310489", "SRX25770930", "SRS22407033", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "DM biol rep 1", "GSM8473257", null, "source name:heads|tissue:heads|genotype:5a / ;5b / |treatment:untreated|geo loc name:missing|collection date:missing", "DM biol rep 1", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a / ;5b / |treatment:untreated", "GSM8473257", "GSM8473257: DM biol rep 1; Danio rerio; RNA Seq", "GSM8473257 r1", "GSM8473257", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47812-DM1_S4_R2_001.fastq.gz Li47812-DM1_S4_R1_001.fastq.gz", "fastq fastq", 5442095245.0, 45006091.0, "GSM8473257 r1", "0:60.48 1:60.44", "A:1406768036;C:1288396960;G:1297715980;T:1439122995;N:10091274", 60, 60, null, null, 1406768036, 1288396960, 1297715980, 1439122995, 10091274, "SRX25770930", "SRS22407033", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94722, 0.95046, 0.09788, 0.09612, 0.63984, 0.6411, 0.46913, 0.4759, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33622, "SRR30310490", "SRX25770929", "SRS22407032", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5b biol rep 3", "GSM8473256", null, "source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing", "5b biol rep 3", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5b / |treatment:untreated", "GSM8473256", "GSM8473256: 5b biol rep 3; Danio rerio; RNA Seq", "GSM8473256 r1", "GSM8473256", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47820-5b3_S12_R2_001.fastq.gz Li47820-5b3_S12_R1_001.fastq.gz", "fastq fastq", 5532330845.0, 45739498.0, "GSM8473256 r1", "0:60.50 1:60.46", "A:1435251569;C:1304605813;G:1312598084;T:1471267089;N:8608290", 60, 60, null, null, 1435251569, 1304605813, 1312598084, 1471267089, 8608290, "SRX25770929", "SRS22407032", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94396, 0.94717, 0.11216, 0.11051, 0.64717, 0.64768, 0.47525, 0.47841, 60, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33623, "SRR30310491", "SRX25770928", "SRS22407031", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5b biol rep 2", "GSM8473255", null, "source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing", "5b biol rep 2", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5b / |treatment:untreated", "GSM8473255", "GSM8473255: 5b biol rep 2; Danio rerio; RNA Seq", "GSM8473255 r1", "GSM8473255", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47819-5b2_S11_R2_001.fastq.gz Li47819-5b2_S11_R1_001.fastq.gz", "fastq fastq", 5530076725.0, 45717614.0, "GSM8473255 r1", "0:60.50 1:60.46", "A:1432780615;C:1306496067;G:1314858379;T:1467817877;N:8123787", 60, 60, null, null, 1432780615, 1306496067, 1314858379, 1467817877, 8123787, "SRX25770928", "SRS22407031", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94205, 0.94641, 0.11508, 0.11379, 0.64788, 0.64672, 0.47602, 0.47695, 61, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33624, "SRR30310492", "SRX25770927", "SRS22407030", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5b biol rep 1", "GSM8473254", null, "source name:heads|tissue:heads|genotype:5b / |treatment:untreated|geo loc name:missing|collection date:missing", "5b biol rep 1", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5b / |treatment:untreated", "GSM8473254", "GSM8473254: 5b biol rep 1; Danio rerio; RNA Seq", "GSM8473254 r1", "GSM8473254", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47818-5b1_S10_R2_001.fastq.gz Li47818-5b1_S10_R1_001.fastq.gz", "fastq fastq", 4784996431.0, 39556747.0, "GSM8473254 r1", "0:60.50 1:60.46", "A:1241886071;C:1129207908;G:1136918789;T:1270031996;N:6951667", 60, 60, null, null, 1241886071, 1129207908, 1136918789, 1270031996, 6951667, "SRX25770927", "SRS22407030", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94373, 0.94771, 0.11067, 0.10905, 0.64729, 0.64583, 0.47752, 0.47625, 59, 60, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33625, "SRR30310493", "SRX25770926", "SRS22407029", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5a biol rep 3", "GSM8473253", null, "source name:heads|tissue:heads|genotype:5a / |treatment:untreated|geo loc name:missing|collection date:missing", "5a biol rep 3", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a / |treatment:untreated", "GSM8473253", "GSM8473253: 5a biol rep 3; Danio rerio; RNA Seq", "GSM8473253 r1", "GSM8473253", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47817-5a3_S9_R2_001.fastq.gz Li47817-5a3_S9_R1_001.fastq.gz", "fastq fastq", 5455669007.0, 45101219.0, "GSM8473253 r1", "0:60.51 1:60.46", "A:1408981430;C:1292361893;G:1307301180;T:1439131814;N:7892690", 60, 60, null, null, 1408981430, 1292361893, 1307301180, 1439131814, 7892690, "SRX25770926", "SRS22407029", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.95182, 0.95421, 0.081, 0.07901, 0.6524, 0.65115, 0.48336, 0.48307, 61, 59, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33626, "SRR30310494", "SRX25770925", "SRS22407028", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5a biol rep 2", "GSM8473252", null, "source name:heads|tissue:heads|genotype:5a / |treatment:untreated|geo loc name:missing|collection date:missing", "5a biol rep 2", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a / |treatment:untreated", "GSM8473252", "GSM8473252: 5a biol rep 2; Danio rerio; RNA Seq", "GSM8473252 r1", "GSM8473252", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47816-5a2_S8_R2_001.fastq.gz Li47816-5a2_S8_R1_001.fastq.gz", "fastq fastq", 5585703633.0, 46182982.0, "GSM8473252 r1", "0:60.50 1:60.45", "A:1439568272;C:1324867892;G:1340137608;T:1471972622;N:9157239", 60, 60, null, null, 1439568272, 1324867892, 1340137608, 1471972622, 9157239, "SRX25770925", "SRS22407028", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.95103, 0.95419, 0.0813, 0.07916, 0.6565, 0.65563, 0.47441, 0.47598, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33627, "SRR30310495", "SRX25770924", "SRS22407027", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "5a biol rep 1", "GSM8473251", null, "source name:heads|tissue:heads|genotype:5a /  |treatment:untreated|geo loc name:missing|collection date:missing", "5a biol rep 1", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:5a /  |treatment:untreated", "GSM8473251", "GSM8473251: 5a biol rep 1; Danio rerio; RNA Seq", "GSM8473251 r1", "GSM8473251", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47815-5a1_S7_R2_001.fastq.gz Li47815-5a1_S7_R1_001.fastq.gz", "fastq fastq", 5421245773.0, 44832660.0, "GSM8473251 r1", "0:60.48 1:60.44", "A:1406624107;C:1276257498;G:1288190603;T:1440236606;N:9936959", 60, 60, null, null, 1406624107, 1276257498, 1288190603, 1440236606, 9936959, "SRX25770924", "SRS22407027", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.9497, 0.95318, 0.08896, 0.08766, 0.64983, 0.65009, 0.46836, 0.46856, 60, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33628, "SRR30310496", "SRX25770923", "SRS22407026", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "WT biol rep 3", "GSM8473250", null, "source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing", "WT biol rep 3", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:WT|treatment:untreated", "GSM8473250", "GSM8473250: WT biol rep 3; Danio rerio; RNA Seq", "GSM8473250 r1", "GSM8473250", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47811-WT3_S3_R2_001.fastq.gz Li47811-WT3_S3_R1_001.fastq.gz", "fastq fastq", 5445129556.0, 45027951.0, "GSM8473250 r1", "0:60.48 1:60.45", "A:1410861744;C:1282813821;G:1294884711;T:1446863056;N:9706224", 60, 60, null, null, 1410861744, 1282813821, 1294884711, 1446863056, 9706224, "SRX25770923", "SRS22407026", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94943, 0.95269, 0.11544, 0.11414, 0.64644, 0.64699, 0.46439, 0.47415, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33629, "SRR30310497", "SRX25770922", "SRS22407025", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "WT biol rep 2", "GSM8473249", null, "source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing", "WT biol rep 2", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:WT|treatment:untreated", "GSM8473249", "GSM8473249: WT biol rep 2; Danio rerio; RNA Seq", "GSM8473249 r1", "GSM8473249", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47810-WT2_S2_R2_001.fastq.gz Li47810-WT2_S2_R1_001.fastq.gz", "fastq fastq", 4788359140.0, 39599012.0, "GSM8473249 r1", "0:60.48 1:60.44", "A:1237189996;C:1129331953;G:1143753687;T:1268980159;N:9103345", 60, 60, null, null, 1237189996, 1129331953, 1143753687, 1268980159, 9103345, "SRX25770922", "SRS22407025", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94746, 0.95043, 0.1121, 0.11092, 0.64411, 0.64342, 0.46922, 0.47301, 59, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [33630, "SRR30310498", "SRX25770921", "SRS22407024", "SRP527479", "PRJNA1150074", "Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling", "GSE275235", "Transcriptome Analysis", "SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants", null, "pubmed:40208862", null, "WT biol rep 1", "GSM8473248", null, "source name:heads|tissue:heads|genotype:WT|treatment:untreated|geo loc name:missing|collection date:missing", "WT biol rep 1", "Fastq files were aligned using STAR and gene counts obtained from STAR were given as input to DESeq2 for differential gene analysis and obtained normalised counts. Genes with zero values in more than 4 samples were exlcuded from the analysis Assembly: GRCz11 Supplementary files format and content: tab delimited text file include raw counts for each sample Supplementary files format and content: tab delimited text file include log normalised counts for each sample", "heads", "untreated", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", "Adult zebrafish TL and AB strains were maintained at 28\u00b0C in a 14 hour light/10 hour dark cycle under standard aquaculture conditions  and fertilized eggs were collected via natural spawning.", "tissue:heads|genotype:WT|treatment:untreated", "GSM8473248", "GSM8473248: WT biol rep 1; Danio rerio; RNA Seq", "GSM8473248 r1", "GSM8473248", "1", "Trizol based RNA extraction and column purification purified RNA with RIN>7 were sent for sequencing NextSeq2000 P2 100 cycle", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP527479", null, null, "Li47809-WT1_S1_R2_001.fastq.gz Li47809-WT1_S1_R1_001.fastq.gz", "fastq fastq", 5047587318.0, 41741097.0, "GSM8473248 r1", "0:60.48 1:60.44", "A:1311031310;C:1185882586;G:1198272234;T:1343072853;N:9328335", 60, 60, null, null, 1311031310, 1185882586, 1198272234, 1343072853, 9328335, "SRX25770921", "SRS22407024", "SRA1951631", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", "Kurrasch Lab, Department of Medical Genetics, University of Calgary", 2, 0.94688, 0.95005, 0.12622, 0.12476, 0.6463, 0.64528, 0.47305, 0.47428, 61, 61, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2024-08-20", "Adult", "Adult", "Head", "Nervous System"], [34192, "SRR31443228", "SRX26812023", "SRS23296672", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 3", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 3", "srrm4[y712] mutant replicate 3", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut3.pass2Aligned.sortedByCoord.out.bam", "bam", 23466336192.0, 117587529.0, "25938 mut3.pass2Aligned.sortedByCoord.out.bam", "0:100.13 1:100.08", "A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927", 100, 100, null, null, 6298034402, 5433884683, 5344985734, 6388443446, 987927, "SRX26812023", "SRS23296672", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.95864, 0.95894, 0.10681, 0.1052, 0.65385, 0.65403, 0.46511, 0.46252, 99, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34193, "SRR31443229", "SRX26812022", "SRS23296671", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 3", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 3", "srrm4[y712] wild type replicate 3", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt3.pass2Aligned.sortedByCoord.out.bam", "bam", 23979171134.0, 120156039.0, "25938 wt3.pass2Aligned.sortedByCoord.out.bam", "0:100.12 1:100.07", "A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857", 100, 100, null, null, 6398807397, 5589997524, 5503127729, 6486232627, 1005857, "SRX26812022", "SRS23296671", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.95941, 0.96004, 0.10323, 0.10191, 0.65451, 0.6532, 0.46396, 0.46398, 101, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34194, "SRR31443230", "SRX26812021", "SRS23296670", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 2", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 2", "srrm4[y712] mutant replicate 2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut2.pass2Aligned.sortedByCoord.out.bam", "bam", 20256127500.0, 101792067.0, "25938 mut2.pass2Aligned.sortedByCoord.out.bam", "0:100.05 1:100.00", "A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366", 100, 100, null, null, 5435798119, 4683997479, 4650293108, 5485187428, 851366, "SRX26812021", "SRS23296670", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.96008, 0.96049, 0.10232, 0.10156, 0.66072, 0.65932, 0.4668, 0.46817, 95, 95, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34195, "SRR31443231", "SRX26812020", "SRS23296669", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 2", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 2", "srrm4[y712] wild type replicate 2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt2.pass2Aligned.sortedByCoord.out.bam", "bam", 22698373371.0, 113599687.0, "25938 wt2.pass2Aligned.sortedByCoord.out.bam", "0:100.18 1:100.12", "A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128", 100, 100, null, null, 6063922145, 5275724786, 5212055837, 6145709475, 961128, "SRX26812020", "SRS23296669", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.96129, 0.96063, 0.1003, 0.09861, 0.65744, 0.65748, 0.46167, 0.46817, 98, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34196, "SRR31443232", "SRX26812019", "SRS23296667", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 1", null, "strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 1", "srrm4[y712] mutant replicate 1", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut.pass2Aligned.sortedByCoord.out.bam", "bam", 11282501509.0, 56702666.0, "25938 mut.pass2Aligned.sortedByCoord.out.bam", "0:99.65 1:99.55", "A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849", 99, 99, null, null, 2764745971, 2868447715, 2856237429, 2792914545, 155849, "SRX26812019", "SRS23296667", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34197, "SRR31443233", "SRX26812018", "SRS23296668", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 1", null, "strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 1", "srrm4[y712] wild type replicate 1", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt.pass2Aligned.sortedByCoord.out.bam", "bam", 16346812838.0, 82104499.0, "25938 wt.pass2Aligned.sortedByCoord.out.bam", "0:99.65 1:99.56", "A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992", 99, 99, null, null, 3996717287, 4167381503, 4130586142, 4051899914, 227992, "SRX26812018", "SRS23296668", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.97776, 0.97907, 0.04095, 0.04006, 0.6702, 0.67034, 0.46611, 0.46144, 99, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "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"]], "truncated": false, "filtered_table_rows_count": 266, "expanded_columns": [], "expandable_columns": [], 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"run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_source\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "TRANSCRIPTOMIC", "p2": "Head"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Head", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 169, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Head&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", 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