RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

266 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Head"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 7

devstage_curation 7

devstage_curation_coarse 4

experiment.library_strategy 3

tissue_curation_coarse 1

tissue_curation 1

  • Head · 266 ✖

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 266 ✖

experiment.library_layout 1

  • PAIRED · 266 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.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
7950 7950 ERR015567 ERX005930 ERS000089 ERP000263 PRJEB2208 Zebrafish gene three prime end pull down for genome annotation E-MTAB-308 Transcriptome Analysis       RNA extracted from male adult zebrafish head   SAMEA708835 SC ENA FIRST PUBLIC:2010 02 26T10:44:13Z|ENA LAST UPDATE:2018 03 08T15:51:30Z|External Id:SAMEA708835|INSDC center name:SC|INSDC first public:2010 02 26T10:44:13Z|INSDC last update:2018 03 08T15:51:30Z|INSDC status:public|Submitter Id:ZF male head sample1|common name:zebrafish|sample name:ZF male head sample1|scientific name:Danio rerio|sex:male|strain:Tuebingen                 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene 3 prime end pull down for genome annotation E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert Zebrafish adult male head mRNA three prime end Zebrafish gene three prime end pull down for genome annotation 20 ug of total RNA was fragmented using RNA Fragmentation Reagent Ambion for 5 minutes at 70 C and ethanol precipitated with glycogen and LiCl. RNA was annealed to the oligo stBPM1polyT22 biotin GGCCAGTCCTGGAGTTTTTTTTTTTTTTTTTTTTTTVN and bound to streptavidin magnetic beads. post washing by pull down on a magnet the bound RNA was reverse transcribed with SuperScript II Invitrogen and a second strand synthesised with DNA polymerase I Promega and RNase H NEB. post further washing the double strand cDNA was released from the beads with BpmI NEB. The cDNA was recovered with the QIAgen PCR Purification Kit and made into a standard Illumina library following the manufacturer's protocol with a fragment size of 250 to 300 bp. Experimental Factor: DEVELOPMENTAL STAGE:adult|Experimental Factor: ORGANISM PART:head|Experimental Factor: SEX:male RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000263 Illumina Genome Analyzer II paired end sequencing; Zebrafish gene three prime end pull down for genome annotation ENA FIRST PUBLIC:2010 08 19|ENA LAST UPDATE:2018 11 16 3444_7.srf srf 1384012896.0 9105348.0 E MTAB 308:Illumina Genome Analyzer II sequencing of adult Zebrafish male head dpf three prime pull down paired end 250 to 300 bp insert 0:76 1:76 A:369912216;C:306963547;G:292249178;T:392053840;N:22834115 76 76     369912216 306963547 292249178 392053840 22834115 ERX005930 ERS000089 ERA010603 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.95932 0.96084 0.20719 0.21321 0.73959 0.74763 0.47227 0.48033 76 76 B B biological fallback assumption illumina early_illumina 3prime other unknown bulk unknown unknown   United Kingdom 2010-02-26 Adult Adult Head Nervous System
8059 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         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                 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   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     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   United Kingdom 2010-02-26 Adult Adult Head Nervous System
8060 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         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                 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   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     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   United Kingdom 2010-02-26 Adult Adult Head Nervous System
11025 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11026 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11027 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11028 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11029 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11030 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11031 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11032 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11033 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11034 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11035 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11036 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11037 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11038 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11039 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
11040 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   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                 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   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     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   Belgium 2022-09-12 Larval Larval Head Nervous System
32068 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.         Kcnd2 Wt 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1933789152 1464135438 1474439143 1900463092 83275 SRX24534635 SRS21280318 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32069 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.         Arfgef1 Hom 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1847018467 1809604703 1818278888 1819707786 121156 SRX24534634 SRS21280317 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32070 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.         Arfgef1 Hom 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1694417387 1616938849 1625276704 1671046414 145846 SRX24534633 SRS21280316 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32071 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.         Arfgef1 Hom 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1739306802 1658195023 1665806667 1714318423 111685 SRX24534632 SRS21280315 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32072 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.         Arfgef1 Het 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1725253563 1652471358 1662793828 1699392429 82322 SRX24534631 SRS21280314 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32073 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.         Arfgef1 Het 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2509621883 2259671963 2271899998 2469380560 238596 SRX24534630 SRS21280313 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32074 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.         Arfgef1 Het 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1766549896 1685533018 1694949682 1740214059 122445 SRX24534629 SRS21280312 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32075 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.         Wnt8b Hom 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2775044850 2525957688 2527072827 2739479844 302691 SRX24534628 SRS21280311 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32076 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.         Wnt8b Hom 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2029345938 1820579149 1819606043 1996786660 488810 SRX24534627 SRS21280310 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32077 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.         Wnt8b Hom 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1711943699 1556010812 1555687818 1690731439 170632 SRX24534626 SRS21280309 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32078 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.         Wnt8b Het 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2360994905 2008091028 2013456743 2332006781 112443 SRX24534625 SRS21280308 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32079 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.         Wnt8b Het 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2275496039 1920819728 1927597917 2246091711 107405 SRX24534624 SRS21280307 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32080 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.         Wnt8b Het 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2059784093 1755740426 1761242316 2037325656 96509 SRX24534623 SRS21280306 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32081 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.         Wnt8b Wt 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1869159615 1548130956 1547169482 1845192460 84987 SRX24534622 SRS21280305 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32082 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.         Arfgef1 Wt 3   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1606427072 1484826935 1488745137 1582299135 65921 SRX24534621 SRS21280304 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32083 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.         Wnt8b Wt 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1852520280 1531023930 1536795067 1823243896 87427 SRX24534620 SRS21280303 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32084 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.         Wnt8b Wt 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1783250074 1493088330 1497228073 1760957638 96285 SRX24534619 SRS21280302 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32085 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.         Kcnd2 Hom 4   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2007694949 1807188755 1800403701 1981369650 317045 SRX24534618 SRS21280301 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32086 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.         Kcnd2 Hom 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2078143741 1581832453 1587225393 2041970189 89324 SRX24534617 SRS21280300 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32087 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.         Kcnd2 Hom 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2185320924 1987553985 1999101969 2159195984 39538 SRX24534616 SRS21280299 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32088 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.         Kcnd2 Het 4   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2675050868 2442920285 2439165482 2638402351 419714 SRX24534615 SRS21280298 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32089 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.         Kcnd2 Het 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1994641167 1795831385 1796069017 1962477823 89408 SRX24534614 SRS21280297 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32090 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.         Kcnd2 Het 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1860484446 1694088253 1695161253 1832038793 84855 SRX24534613 SRS21280296 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32091 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.         Kcnd2 Wt 4   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     2136890254 1951822302 1947544318 2105854363 335463 SRX24534612 SRS21280295 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32092 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.         Kcnd2 Wt 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1902466623 1451301657 1460696794 1874184765 30761 SRX24534611 SRS21280294 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32093 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.         Arfgef1 Wt 2   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1904125951 1807905407 1812898141 1874904149 147852 SRX24534610 SRS21280293 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32094 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.         Arfgef1 Wt 1   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                 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.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507312     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     1927852618 1855757148 1860100302 1898222485 124747 SRX24534609 SRS21280292 SRA1864976 Boston Childrens Hospital|Neurobiology Boston Childrens Hospital                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2024-05-13 Larval Larval Head Nervous System
32098 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 fa…       Chondrocyte head biolRep3 GSM8264152   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     1843991471 1548648708 1568393744 1858508350 106120 SRX24535482 SRS21281082 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32099 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 fa…       Chondrocyte head biolRep2 GSM8264151   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     1697207927 1464700434 1476121489 1690068467 279517 SRX24535481 SRS21281081 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32100 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 fa…       Chondrocyte head biolRep1 GSM8264150   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     956150712 837180050 846748291 954113728 156586 SRX24535480 SRS21281080 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32104 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 fa…       Osteoblast head biolRep3 GSM8264146   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     1091466642 915105554 923772050 1085593417 164161 SRX24535476 SRS21281076 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32105 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 fa…       Osteoblast head biolRep2 GSM8264145   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     1007186967 837532125 846083342 1001209204 160866 SRX24535475 SRS21281075 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32106 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 fa…       Osteoblast head biolRep1 GSM8264144   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   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.   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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP507332   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     2308551585 1841082082 2161425693 2253505108 4829888 SRX24535474 SRS21281074 SRA1865629 Institute for Cardiovascular Organogenesis and Regeneration Institute for Cardiovascular Organogenesis and Regeneration                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2024-05-13 Larval Larval Head Nervous System
32806 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 sever…   pubmed:39289367   head scarb2a mut rep 3 GSM8339369   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32807 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 sever…   pubmed:39289367   head scarb2a mut rep 2 GSM8339368   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32808 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 sever…   pubmed:39289367   head scarb2a mut rep 1 GSM8339367   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32809 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 sever…   pubmed:39289367   head wt rep 4 GSM8339366   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32810 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 sever…   pubmed:39289367   head wt rep 3 GSM8339365   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
32811 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 sever…   pubmed:39289367   head wt rep 1 GSM8339364   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   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   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 70µm filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 µl 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 70µm nozzle. RNA was captured using Dynabeads™ mRNA DIRECT™ 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.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP515053     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     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   75 8 B T sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate marsseq   Israel 2024-06-20 Hatching Embryo Head Nervous System
33619 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 …   pubmed:40208862   DM biol rep 3 GSM8473259   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33620 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 …   pubmed:40208862   DM biol rep 2 GSM8473258   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33621 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 …   pubmed:40208862   DM biol rep 1 GSM8473257   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33622 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 …   pubmed:40208862   5b biol rep 3 GSM8473256   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33623 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 …   pubmed:40208862   5b biol rep 2 GSM8473255   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33624 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 …   pubmed:40208862   5b biol rep 1 GSM8473254   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33625 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 …   pubmed:40208862   5a biol rep 3 GSM8473253   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33626 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 …   pubmed:40208862   5a biol rep 2 GSM8473252   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33627 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 …   pubmed:40208862   5a biol rep 1 GSM8473251   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33628 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 …   pubmed:40208862   WT biol rep 3 GSM8473250   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33629 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 …   pubmed:40208862   WT biol rep 2 GSM8473249   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
33630 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 …   pubmed:40208862   WT biol rep 1 GSM8473248   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°C 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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 2000   SRP527479     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     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   Canada 2024-08-20 Adult Adult Head Nervous System
34192 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         srrm4[y712] mutant replicate 3   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                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 3 srrm4[y712] mutant replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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   United States 2024-11-22 Larval Larval Head Nervous System
34193 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         srrm4[y712] wild type replicate 3   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                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 3 srrm4[y712] wild type replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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   United States 2024-11-22 Larval Larval Head Nervous System
34194 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         srrm4[y712] mutant replicate 2   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                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 2 srrm4[y712] mutant replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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   United States 2024-11-22 Larval Larval Head Nervous System
34195 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         srrm4[y712] wild type replicate 2   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                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 2 srrm4[y712] wild type replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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   United States 2024-11-22 Larval Larval Head Nervous System
34196 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         srrm4[y712] mutant replicate 1   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                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 1 srrm4[y712] mutant replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34197 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         srrm4[y712] wild type replicate 1   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                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 1 srrm4[y712] wild type replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   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     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   United States 2024-11-22 Larval Larval Head Nervous System
34712 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.       Well P1 05H GSM8775334   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   210 74 47 101 0 SRX27573024 SRS23984677 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34713 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.       Well P1 05G GSM8775333   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   602824 246794 422064 471661 2321 SRX27573023 SRS23984676 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34714 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.       Well P1 05F GSM8775332   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   32466011 9391164 14603239 18226855 106091 SRX27573022 SRS23984675 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34715 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.       Well P1 05E GSM8775331   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   7745921 3203071 7199342 5360465 31457 SRX27573021 SRS23984674 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34716 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.       Well P1 05D GSM8775330   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   44069791 12867012 18935172 25657047 141890 SRX27573020 SRS23984673 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34717 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.       Well P1 05C GSM8775329   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   9098221 3194198 6516993 5738665 35411 SRX27573019 SRS23984672 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34718 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.       Well P1 05B GSM8775328   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   146424611 46287832 64801496 88677718 489255 SRX27573018 SRS23984671 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34719 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.       Well P1 05A GSM8775327   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   5712677 2316258 5388122 3975276 22355 SRX27573017 SRS23984670 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34720 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.       Well P1 12H GSM8775389   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   70 25 61 36 0 SRX27573016 SRS23984669 SRA2070568 UMass Chan UMass Chan                       T   under 1.2% mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34721 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.       Well P1 12G GSM8775388   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   2531 932 1152 1529 0 SRX27573015 SRS23984668 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34722 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.       Well P1 12F GSM8775387   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   192 67 130 139 0 SRX27573014 SRS23984666 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34723 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.       Well P1 12E GSM8775386   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   84224 34420 85992 62126 550 SRX27573013 SRS23984667 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34724 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.       Well P1 12D GSM8775385   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   2133794 938571 2850027 1703116 9324 SRX27573012 SRS23984665 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34725 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.       Well P1 12C GSM8775384   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   3753240 1715145 4579242 2889684 17745 SRX27573011 SRS23984664 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34726 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.       Well P1 12B GSM8775383   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   3385725 1544608 4301274 2699465 16560 SRX27573010 SRS23984663 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34727 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.       Well P1 08H GSM8775358   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   114 44 65 65 0 SRX27573009 SRS23984662 SRA2070568 UMass Chan UMass Chan                       T   under 1.2% mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34728 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.       Well P1 08G GSM8775357   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   8706380 3262708 7330788 5889373 36047 SRX27573008 SRS23984661 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34729 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.       Well P1 08F GSM8775356   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   10289406 3851867 8139616 6575750 40465 SRX27573007 SRS23984660 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34730 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.       Well P1 08E GSM8775355   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   6595819 2847582 6802285 4838399 28523 SRX27573006 SRS23984659 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34731 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.       Well P1 08D GSM8775354   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   4392257 1994475 7440459 3596074 22383 SRX27573005 SRS23984658 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34732 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.       Well P1 08C GSM8775353   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   4629476 2009722 5052427 3434235 20156 SRX27573004 SRS23984656 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34733 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.       Well P1 08B GSM8775352   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   1191235462 707748234 767219572 1075959763 5324025 SRX27573003 SRS23984657 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34734 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.       Well P1 08A GSM8775351   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   5780741 2263389 5259112 3921095 23023 SRX27573002 SRS23984655 SRA2070568 UMass Chan UMass Chan                       B   usable mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System
34735 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.       Well P1 04H GSM8775326   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   tiny sci sci RNA seq protocol Three heads per biological replicate and three biological replicates per genotype were pooled in 100 µl 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°C using a Bioruptor® 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 “Tiny Sci” 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 µl 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°C using a Bioruptor® 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.   OTHER TRANSCRIPTOMIC other PAIRED ILLUMINA NextSeq 500   SRP561592   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   877 264 476 495 0 SRX27573001 SRS23984654 SRA2070568 UMass Chan UMass Chan                       T   under 1.2% mapping rate illumina nextseq unknown other unknown sc single_cell_plate scirnaseq   United States 2025-02-04 Larval Larval Head Nervous System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;