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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,SRR29008446,SRX24535482,SRS21281082,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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,SRR29008447,SRX24535481,SRS21281081,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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,SRR29008448,SRX24535480,SRS21281080,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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,SRR29008452,SRX24535476,SRS21281076,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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,SRR29008453,SRX24535475,SRS21281075,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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,SRR29008454,SRX24535474,SRS21281074,SRP507332,PRJNA1111082,Integration of ATAC and RNA Sequencing identifies chromatin and transcriptomic signatures in classical and non classical zebrafish osteoblasts and indicates mechanisms of entpd5a regulation [RNA],GSE267333,Transcriptome Analysis,Two types of osteoblasts are required to assemble the zebrafish embryonic skeleton: classical osteoblasts homologous to the mammalian situation  and notochord sheath cells  which serve as non classical osteoblasts. The gene entpd5a is critically required for ossification via both types of osteoblasts. Despite the usefulness of zebrafish models in vertebrate research  the genetic regulation of bone formation  as well as mechanisms of transcriptional control of entpd5a  remain largely unknown. Here  using a newly generated transgenic line  we isolate classical and non classical osteoblasts from zebrafish embryos and performed both ATAC Seq and RNA Seq. We analysed results independently and integratively to understand those chromatin dynamics and accompanying transcriptomic changes that occur in different skeletal cells. We show that although Dlx family factors are playing important roles in classical osteoblast regulation  Hox family factors are involved in governing spinal ossification via non classical osteoblasts. We further present a resource driven analysis of the entpd5a promoter  experimentally validating the ATAC Seq dataset and proposing mechanisms of regulating the complex entpd5a expression pattern during zebrafish osteogenesis. Our results thus provide a necessary comprehensive resource for the field of bone development and indicate spatio temporally regulated promoter/enhancer interactions taking place in the entpd5a locus. Overall design: We used the newly generated entpd5a:Gal4FF;UAS:GFP;R2col2a1a:mCherry transgenic line to isolate via FACS head classical and trunk non classical osteoblasts from zebrafish embryos at 15dpf. We also extracted adjacent head cartilage and intersegmental spinal chondrocytes as controls. With these four isolated cell populations we performed both ATAC Seq and RNA Seq and analysed data at first individually  to establish open chromatin regions and gene expression profiles  respectively. We then integrated the data to enable us to produce a list of candidate transcription factors likely to function in vivo in each of the cell types during zebrafish skeletogenesis.,,,,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
33619,SRR30310487,SRX25770932,SRS22407035,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310488,SRX25770931,SRS22407034,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310489,SRX25770930,SRS22407033,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310490,SRX25770929,SRS22407032,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310491,SRX25770928,SRS22407031,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310492,SRX25770927,SRS22407030,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310493,SRX25770926,SRS22407029,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310494,SRX25770925,SRS22407028,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310495,SRX25770924,SRS22407027,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310496,SRX25770923,SRS22407026,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310497,SRX25770922,SRS22407025,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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,SRR30310498,SRX25770921,SRS22407024,SRP527479,PRJNA1150074,Epileptic phenotypes in slc13a5 loss of function zebrafish are rescued by blocking NMDA receptor signaling,GSE275235,Transcriptome Analysis,SLC13A5 encodes a citrate transporter highly expressed in the brain important for regulating intra  and extracellular citrate levels. Mutations in this gene cause a rare infantile epilepsy characterized by lifelong seizures  developmental delays  behavioral deficits  poor motor progression  and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here  we used CRISPR/Cas9 to create loss of function mutations in slc13a5a and slc13a5b  the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances  consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum  a region important for sensory processing. slc13a5 mutants displayed hallmark features of epilepsy  including an imbalance in glutamatergic and GABAergic excitatory inhibitory gene expression  disrupted neurometabolism  and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically  we tested the involvement of NMDA signaling in slc13a5 mutant epilepsy like phenotypes. Slc13a5 protein co localizes with excitatory NMDA receptors in wild type zebrafish and blocking NMDA receptors in slc13a5 mutant larvae rescued bioenergetics  hyperexcitable calcium events  and behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over chelates the ions needed to regulate NMDA receptor function  leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery. Overall design: 5 dpf zebrafish heads were pooled to generate three biological replicates of each group. Four groups of samples were generated: WT controls  5a mutants  5b mutants and 5a/5b double mutants,,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
37210,SRR1028004,SRX376581,SRS501207,SRP032838,PRJNA227277,Danio rerio Transcriptome or Gene expression,PRJNA227277,Other,transcriptome analysis of zebrafish whole head.,,,wild type zebrafish sample 3,Wt 3,iiina,,label:3|age:6 days|tissue type:whole head,,,,,,,,,Transcriptome analysis of zebrafish's whole head.,ZF na   iiina,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP032838,,,iiina_1.fastq.tar.gz iiina_2.fastq.tar.gz,fastq fastq,4316715356.0,21369878.0,iiina,0:101 1:101,A:1146719253;C:995646710;G:1009198100;T:1125396496;N:39754797,101,101,,,1146719253,995646710,1009198100,1125396496,39754797,SRX376581,SRS501207,SRA110728,BIU|Levanon,BIU,2,0.92916,0.92726,0.08723,0.0948,0.65514,0.68923,0.47003,0.47006,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2014-11-11,Larval,Larval,Head,Nervous System
37211,SRR1028003,SRX376580,SRS501206,SRP032838,PRJNA227277,Danio rerio Transcriptome or Gene expression,PRJNA227277,Other,transcriptome analysis of zebrafish whole head.,,,wild type zebrafish sample 2,Wt 2,iina,,label:2|age:6 days|tissue type:whole head,,,,,,,,,Transcriptome analysis of zebrafish's whole head.,ZF na   iina,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP032838,,,iina_1.fastq.tar.gz iina_2.fastq.tar.gz,fastq fastq,4955839518.0,24533859.0,iina,0:101 1:101,A:1280850150;C:1179933762;G:1174869989;T:1275240888;N:44944729,101,101,,,1280850150,1179933762,1174869989,1275240888,44944729,SRX376580,SRS501206,SRA110728,BIU|Levanon,BIU,2,0.93499,0.9343,0.07143,0.07615,0.65427,0.67233,0.47221,0.47326,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2014-11-11,Larval,Larval,Head,Nervous System
37212,SRR1028002,SRX375515,SRS501219,SRP032838,PRJNA227277,Danio rerio Transcriptome or Gene expression,PRJNA227277,Other,transcriptome analysis of zebrafish whole head.,,,wild type zebrafish sample 1,Wt 1,ina,,label:1|age:6 days|tissue type:whole head,,,,,,,,,Transcriptome analysis of zebrafish's whole head.,ZF na   ina,1,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP032838,,,ina_2.fastq.tar.gz ina_1.fastq.tar.gz,fastq fastq,5519994006.0,27326703.0,ina 1,0:101 1:101,A:1456361266;C:1288156090;G:1276246591;T:1448748282;N:50481777,101,101,,,1456361266,1288156090,1276246591,1448748282,50481777,SRX375515,SRS501219,SRA110728,BIU|Levanon,BIU,2,0.92874,0.9272,0.08523,0.09251,0.65445,0.67681,0.47526,0.47863,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Israel,2014-11-11,Larval,Larval,Head,Nervous System
38299,SRR1648856,SRX757983,SRS743130,SRP049716,PRJNA266970,RNA sequencing of the developing zebrafish head,GSE63191,Transcriptome Analysis,We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain,,pubmed:25561519,,Wildtype Replicate 3,GSM1543674,,source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head,Wildtype Replicate 3,Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking,whole head,,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf  the heads of 80 100 embryos per replicate were obtained for RNA extraction.,develolpmental stage:5 dpf embryo|tissue:whole head,GSM1543674,GSM1543674: Wildtype Replicate 3; Danio rerio; RNA Seq,GSM1543674,,1,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,GEO Accession:GSM1543674,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP049716,,,uninjected_rep3_zebrafish_121230_AC1BMGACXX_Illumina8_1.fastq.gz uninjected_rep3_zebrafish_121230_AC1BMGACXX_Illumina8_2.fastq.gz,fastq fastq,7947025900.0,79470259.0,GSM1543674 r1,0:50 1:50,A:2171440033;C:1752204345;G:1782154451;T:2240911661;N:315410,50,50,,,2171440033,1752204345,1782154451,2240911661,315410,SRX757983,SRS743130,SRA200859,GEO,"Center for Human Genetic Research, Massachusetts General Hospital",2,0.92472,0.92889,0.15282,0.15037,0.72015,0.71969,0.47465,0.48174,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2014-11-12,Larval,Larval,Head,Nervous System
38300,SRR1648855,SRX757982,SRS743129,SRP049716,PRJNA266970,RNA sequencing of the developing zebrafish head,GSE63191,Transcriptome Analysis,We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain,,pubmed:25561519,,Wildtype Replicate 2,GSM1543673,,source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head,Wildtype Replicate 2,Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking,whole head,,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf  the heads of 80 100 embryos per replicate were obtained for RNA extraction.,develolpmental stage:5 dpf embryo|tissue:whole head,GSM1543673,GSM1543673: Wildtype Replicate 2; Danio rerio; RNA Seq,GSM1543673,,1,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,GEO Accession:GSM1543673,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP049716,,,uninjected_rep2_zebrafish_121230_AC1BMGACXX_Illumina5_2.fastq.gz uninjected_rep2_zebrafish_121230_AC1BMGACXX_Illumina5_1.fastq.gz,fastq fastq,7400831800.0,74008318.0,GSM1543673 r1,0:50 1:50,A:1997686488;C:1645601571;G:1723353684;T:2033898648;N:291409,50,50,,,1997686488,1645601571,1723353684,2033898648,291409,SRX757982,SRS743129,SRA200859,GEO,"Center for Human Genetic Research, Massachusetts General Hospital",2,0.90663,0.91107,0.33386,0.33587,0.7153,0.71553,0.48819,0.49079,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2014-11-12,Larval,Larval,Head,Nervous System
38301,SRR1648854,SRX757981,SRS743128,SRP049716,PRJNA266970,RNA sequencing of the developing zebrafish head,GSE63191,Transcriptome Analysis,We sequenced strand specific mRNA from the heads of 3 groups of wild type zebrafish Danio rerio 5 dpf Overall design: Examination of the relative expression of genes in the developing zebrafish brain,,pubmed:25561519,,Wildtype Replicate 1,GSM1543672,,source name:whole head|develolpmental stage:5 dpf embryo|tissue:whole head,Wildtype Replicate 1,Basecalls performed using CASAVA version 1.5 Alignment was performed with Gsnap v2012 07 20 using default parameters and the zv9 genome/transcriptome from Ensembl Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike ins Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl Genome build: zv9 Supplementary files format and content: Cufflinks v2.1.0 genes.fpkm tracking,whole head,,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 dpf  the heads of 80 100 embryos per replicate were obtained for RNA extraction.,develolpmental stage:5 dpf embryo|tissue:whole head,GSM1543672,GSM1543672: Wildtype Replicate 1; Danio rerio; RNA Seq,GSM1543672,,1,TRIzol Invitrogen extraction per manufactor's instructions Strand specific  polyA selected RNA Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols  with the addition of 1ul of a 1:10 dilution of ERCC RNA spike ins prior to polyA selection.,GEO Accession:GSM1543672,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP049716,,,uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_1.fastq.gz uninjected_rep1_zebrafish_121230_AC1BMGACXX_Illumina2_2.fastq.gz,fastq fastq,5994627800.0,59946278.0,GSM1543672 r1,0:50 1:50,A:1649718236;C:1309696705;G:1340401079;T:1694576298;N:235482,50,50,,,1649718236,1309696705,1340401079,1694576298,235482,SRX757981,SRS743128,SRA200859,GEO,"Center for Human Genetic Research, Massachusetts General Hospital",2,0.9191,0.92223,0.18431,0.18241,0.68889,0.68793,0.48942,0.48534,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2014-11-12,Larval,Larval,Head,Nervous System
39641,SRR2029856,SRX1030037,SRS938363,SRP058038,PRJNA283169,Danio rerio Raw sequence reads,PRJNA283169,Other,RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.,,,RNA was purified from WT 6dpf zebrafish larvae,WT whole head larva zebrafish,WT,,breed:AB|dev stage:6 dpf|sex:pooled male and female|tissue:whole head|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a,WT 5,WT 5,Biological replicate 5,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP058038,,,Sample_ii-na_2.fastq Sample_ii-na_1.fastq,fastq fastq,4970948000.0,24854740.0,WT 5,0:100 1:100,A:1326071248;C:1167369974;G:1133391102;T:1318946364;N:25169312,100,100,,,1326071248,1167369974,1133391102,1318946364,25169312,SRX1030037,SRS938363,SRA266465,Bar Ilan University|Dr. Lior Appelbaum,Bar Ilan University,2,0.93711,0.93844,0.07857,0.07934,0.64613,0.64711,0.47852,0.47693,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Israel,2016-05-06,Larval,Larval,Head,Nervous System
39642,SRR2025058,SRX1030036,SRS938363,SRP058038,PRJNA283169,Danio rerio Raw sequence reads,PRJNA283169,Other,RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.,,,RNA was purified from WT 6dpf zebrafish larvae,WT whole head larva zebrafish,WT,,breed:AB|dev stage:6 dpf|sex:pooled male and female|tissue:whole head|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a,WT 4,WT 4,Biological replicate 4,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP058038,,loader:latf load,Sample_i-na_1.fastq Sample_i-na_2.fastq,fastq fastq,2622392600.0,26223926.0,WT 4,0:100,A:713649918;C:606120888;G:578652870;T:712333113;N:11635811,100,,,,713649918,606120888,578652870,712333113,11635811,SRX1030036,SRS938363,SRA266465,Bar Ilan University|Dr. Lior Appelbaum,Bar Ilan University,1,0.93312,,0.09652,,0.64758,,0.47024,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Israel,2016-05-06,Larval,Larval,Head,Nervous System
39643,SRR2025020,SRX1030035,SRS938363,SRP058038,PRJNA283169,Danio rerio Raw sequence reads,PRJNA283169,Other,RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.,,,RNA was purified from WT 6dpf zebrafish larvae,WT whole head larva zebrafish,WT,,breed:AB|dev stage:6 dpf|sex:pooled male and female|tissue:whole head|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a,WT 3,WT 3,Biological replicate 3,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP058038,,loader:latf load,Sample_iii-a_2.fastq Sample_iii-a_1.fastq,fastq fastq,2578775300.0,25787753.0,WT 3,0:100,A:710064453;C:580284486;G:570277437;T:702861739;N:15287185,100,,,,710064453,580284486,570277437,702861739,15287185,SRX1030035,SRS938363,SRA266465,Bar Ilan University|Dr. Lior Appelbaum,Bar Ilan University,1,0.92355,,0.11281,,0.64346,,0.47868,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Israel,2016-05-06,Larval,Larval,Head,Nervous System
39644,SRR2025004,SRX1030034,SRS938363,SRP058038,PRJNA283169,Danio rerio Raw sequence reads,PRJNA283169,Other,RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.,,,RNA was purified from WT 6dpf zebrafish larvae,WT whole head larva zebrafish,WT,,breed:AB|dev stage:6 dpf|sex:pooled male and female|tissue:whole head|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a,WT 2,WT 2,Biological replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP058038,,loader:latf load,,,5748638600.0,57486386.0,WT 2,0:100,A:1582673281;C:1315049990;G:1252719550;T:1572983229;N:25212550,100,,,,1582673281,1315049990,1252719550,1572983229,25212550,SRX1030034,SRS938363,SRA266465,Bar Ilan University|Dr. Lior Appelbaum,Bar Ilan University,1,0.93088,,0.09912,,0.64439,,0.4756,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Israel,2015-05-18,Larval,Larval,Head,Nervous System
39645,SRR2025001,SRX1030032,SRS938363,SRP058038,PRJNA283169,Danio rerio Raw sequence reads,PRJNA283169,Other,RNA sequencing of whole head and Hcrt cells of 6dpf larvae zebrafish.,,,RNA was purified from WT 6dpf zebrafish larvae,WT whole head larva zebrafish,WT,,breed:AB|dev stage:6 dpf|sex:pooled male and female|tissue:whole head|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptional profiling of hypocretin neurons identifies the sleep regulator Kcnh4a,WT 1,WT 1,RNA was purified from 6dpf WT larvae zebrafish. Biological replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP058038,,loader:latf load,,,2116790100.0,21167901.0,WT 1,0:100,A:574102889;C:484943445;G:475977813;T:569490955;N:12274998,100,,,,574102889,484943445,475977813,569490955,12274998,SRX1030032,SRS938363,SRA266465,Bar Ilan University|Dr. Lior Appelbaum,Bar Ilan University,1,0.93025,,0.10052,,0.64398,,0.47695,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Israel,2015-05-18,Larval,Larval,Head,Nervous System
40494,SRR3204724,SRX1614066,SRS1323928,SRP070923,PRJNA313387,Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.,PRJNA313387,Other,RNA libraries were constructed from control  6.25 and 12.5 mg/L treatment groups  respectively. post DKAs exposure to 3 mpf zebrafish  the whole transcriptome was determined.,,,12.5 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin  ciprofloxacin  enrofloxacin  doxycycline  chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf,12.5mg/L DKAs,T21,,strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish  i.e. removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems.|treatment:12.5 mg/L DKAs exposure|BioSampleModel:Model organism or animal,,,,,,,,,12.5mg/L DKAs,T21,1,Zebrafish in 12.5 mg/L β diketone antibiotics  treatment groupwith equal weight concentrations and volumes for ofloxacin  ciprofloxacin  enrofloxacin  doxycycline  chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf  and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish  i.e.  removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems. The retained tissues were used to extract total RNA  using Trizol Invitrogen  Carlsbad  CA  USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent  Santa Clara  CA  USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina  San Diego  USA  and the average 300±50 bp insert size was used for the paired end libraries. Finally  the paired end sequencing was performed on an Illumina Hiseq2000/2500.    Prior to assembly  the low quality reads 1  reads containing sequencing adaptors; 2  reads containing sequencing primer; 3  nucleotide with q scores lower than 20 were removed. Next  the cleaned and paired end reads were produced.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070923,,,T21_Clean_Data1.fq.gz T21_Clean_Data2.fq.gz,fastq fastq,10502615500.0,42010462.0,T21,0:125 1:125,A:2848309151;C:2371408734;G:2356749579;T:2925931092;N:216944,125,125,,,2848309151,2371408734,2356749579,2925931092,216944,SRX1614066,SRS1323928,SRA359545,School of Life Sciences,School of Life Sciences,2,0.87768,0.88612,0.29688,0.29743,0.68738,0.68363,0.52932,0.52507,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,unknown,unknown,,Unknown,2016-03-16,Adult,Adult,Head,Nervous System
40495,SRR3203073,SRX1612569,SRS1321766,SRP070923,PRJNA313387,Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.,PRJNA313387,Other,RNA libraries were constructed from control  6.25 and 12.5 mg/L treatment groups  respectively. post DKAs exposure to 3 mpf zebrafish  the whole transcriptome was determined.,,,6.25 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin  ciprofloxacin  enrofloxacin  doxycycline  chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf,6.25mg/L DKAs,T11,,strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish  i.e. removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems.|treatment:6.25 mg/L DKAs exposure|BioSampleModel:Model organism or animal,,,,,,,,,6.25 mg/L DKAs,T11,1,Zebrafish in 6.25 mg/L β diketone antibiotics  treatment groupwith equal weight concentrations and volumes for ofloxacin  ciprofloxacin  enrofloxacin  doxycycline  chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf  and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish  i.e.  removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems. The retained tissues were used to extract total RNA  using Trizol Invitrogen  Carlsbad  CA  USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent  Santa Clara  CA  USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina  San Diego  USA  and the average 300±50 bp insert size was used for the paired end libraries. Finally  the paired end sequencing was performed on an Illumina Hiseq2000/2500.    Prior to assembly  the low quality reads 1  reads containing sequencing adaptors; 2  reads containing sequencing primer; 3  nucleotide with q scores lower than 20 were removed. Next  the cleaned and paired end reads were produced.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070923,,,T11_Clean_Data1.fq.gz T11_Clean_Data2.fq.gz,fastq fastq,8178356500.0,32713426.0,T11,0:125 1:125,A:2135090304;C:1929011381;G:1912585084;T:2201518295;N:151436,125,125,,,2135090304,1929011381,1912585084,2201518295,151436,SRX1612569,SRS1321766,SRA359545,School of Life Sciences,School of Life Sciences,2,0.84003,0.84827,0.32283,0.32402,0.71031,0.70502,0.58398,0.58631,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,unknown,unknown,,Unknown,2016-03-15,Adult,Adult,Head,Nervous System
40496,SRR3195594,SRX1604653,SRS1314385,SRP070923,PRJNA313387,Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.,PRJNA313387,Other,RNA libraries were constructed from control  6.25 and 12.5 mg/L treatment groups  respectively. post DKAs exposure to 3 mpf zebrafish  the whole transcriptome was determined.,,,,,zebrafish,,strain:AB strain|isolate:Oregon State University|breed:Danio rerio|cultivar:not applicable|ecotype:Wild type|age:3 mpf|dev stage:3 mpf|sex:pooled male and female|tissue:we performed simple anatomy of the whole fish  i.e.  removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems.|BioSampleModel:Model organism or animal,,,,,,,,,control,CON 01,1,Zebrafish in control group were randomly selected post DKAs exposure at 90 dpf  and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish  i.e.  removing gill  fin and tail tissue  while retaining visceral mass  head  spine and other nerve systems. The retained tissues were used to extract total RNA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent  Santa Clara  CA  USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina  San Diego  USA  and the average 300±50 bp insert size was used for the paired end libraries. Finally  the paired end sequencing was performed on an Illumina Hiseq2000/2500.    Prior to assembly  the low quality reads 1  reads containing sequencing adaptors; 2  reads containing sequencing primer; 3  nucleotide with q scores lower than 20 were removed. Next  the cleaned and paired end reads were produced.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070923,,,CON_01_Clean_Data2.fq.gz CON_01_Clean_Data1.fq.gz,fastq fastq,8941582750.0,35766331.0,control,0:125 1:125,A:2282842470;C:2172817074;G:2169521320;T:2316254609;N:147277,125,125,,,2282842470,2172817074,2169521320,2316254609,147277,SRX1604653,SRS1314385,SRA359545,School of Life Sciences,School of Life Sciences,2,0.62865,0.62758,0.22408,0.21961,0.7525,0.75024,0.5332,0.519,125,125,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,unknown,bulk,unknown,unknown,,Unknown,2016-03-15,Adult,Adult,Head,Nervous System
47711,SRR6829416,SRX3785505,SRS3038469,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch neg rep3,GSM3039489,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,notch neg rep3,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,GSM3039489,GSM3039489: notch neg rep3; Danio rerio; RNA Seq,GSM3039489,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039489,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,neg-neg-13-05-mix1_S5_all_R1_001_egal.fastq.gz neg-neg-13-05-mix1_S5_all_R2_001_egal.fastq.gz,fastq fastq,11746047446.0,59873586.0,GSM3039489 r1,0:98.09 1:98.09,A:3771210735;C:2134333892;G:2150989811;T:3680038894;N:9474114,98,98,,,3771210735,2134333892,2150989811,3680038894,9474114,SRX3785505,SRS3038469,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.88236,0.88293,0.35343,0.35222,0.72991,0.73068,0.48238,0.48093,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
47712,SRR6829415,SRX3785504,SRS3038467,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch neg rep2,GSM3039488,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,notch neg rep2,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,GSM3039488,GSM3039488: notch neg rep2; Danio rerio; RNA Seq,GSM3039488,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039488,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,neg-neg-30-04-mix1_S3_all_R1_001_egal.fastq.gz neg-neg-30-04-mix1_S3_all_R2_001_egal.fastq.gz,fastq fastq,7126756519.0,36714322.0,GSM3039488 r1,0:97.04 1:97.07,A:2322741127;C:1262806177;G:1289601518;T:2245830796;N:5776901,97,97,,,2322741127,1262806177,1289601518,2245830796,5776901,SRX3785504,SRS3038467,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.8676,0.86758,0.43928,0.4374,0.7218,0.7221,0.47374,0.46588,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
47713,SRR6829414,SRX3785503,SRS3038466,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch neg rep1,GSM3039487,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,notch neg rep1,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:Notch3 mutant|cell types:radial glia,GSM3039487,GSM3039487: notch neg rep1; Danio rerio; RNA Seq,GSM3039487,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039487,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,neg-neg-17-04-mix2_S1_all_R1_001_egal.fastq.gz neg-neg-17-04-mix2_S1_all_R2_001_egal.fastq.gz,fastq fastq,10781166014.0,55053561.0,GSM3039487 r1,0:97.91 1:97.92,A:3498272835;C:1933084814;G:1959130274;T:3382140317;N:8537774,97,97,,,3498272835,1933084814,1959130274,3382140317,8537774,SRX3785503,SRS3038466,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.87032,0.86858,0.40699,0.4038,0.71348,0.71332,0.494,0.46382,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
47714,SRR6829413,SRX3785502,SRS3038468,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch pos rep3,GSM3039486,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,notch pos rep3,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,GSM3039486,GSM3039486: notch pos rep3; Danio rerio; RNA Seq,GSM3039486,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039486,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,pos-pos-13-05-mix2_S6_all_R1_001_egal.fastq.gz pos-pos-13-05-mix2_S6_all_R2_001_egal.fastq.gz,fastq fastq,10945039013.0,55911072.0,GSM3039486 r1,0:97.87 1:97.88,A:3540619715;C:1970835490;G:1993028621;T:3431897779;N:8657408,97,97,,,3540619715,1970835490,1993028621,3431897779,8657408,SRX3785502,SRS3038468,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.88288,0.88076,0.36866,0.36499,0.72723,0.72788,0.49143,0.47893,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
47715,SRR6829412,SRX3785501,SRS3038465,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch pos rep2,GSM3039485,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,notch pos rep2,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,GSM3039485,GSM3039485: notch pos rep2; Danio rerio; RNA Seq,GSM3039485,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039485,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,pos-pos-30-04-mix2_S4_all_R1_001_egal.fastq.gz pos-pos-30-04-mix2_S4_all_R2_001_egal.fastq.gz,fastq fastq,6845715459.0,35221236.0,GSM3039485 r1,0:97.18 1:97.18,A:2206040368;C:1235690694;G:1254535206;T:2143962099;N:5487092,97,97,,,2206040368,1235690694,1254535206,2143962099,5487092,SRX3785501,SRS3038465,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.86571,0.86449,0.43078,0.42846,0.71804,0.71865,0.48512,0.48589,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
47716,SRR6829411,SRX3785500,SRS3038464,SRP135259,PRJNA438111,RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells,GSE111765,Transcriptome Analysis,The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.,,pubmed:29695612,,notch pos rep1,GSM3039484,,source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,notch pos rep1,basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.,head  without xxx,,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia,GSM3039484,GSM3039484: notch pos rep1; Danio rerio; RNA Seq,GSM3039484,,1,The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3039484,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP135259,,,pos-pos-17-04-mix1_S2_all_R1_001_egal.fastq.gz pos-pos-17-04-mix1_S2_all_R2_001_egal.fastq.gz,fastq fastq,10302973813.0,52489402.0,GSM3039484 r1,0:98.14 1:98.15,A:3331056733;C:1851923955;G:1872031048;T:3239709185;N:8252892,98,98,,,3331056733,1851923955,1872031048,3239709185,8252892,SRX3785500,SRS3038464,SRA666168,GEO,"Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris",2,0.88173,0.88043,0.36084,0.35676,0.70794,0.70936,0.49847,0.4986,100,100,B,B,biological fallback assumption,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,France,2018-03-13,Larval,Larval,Head,Nervous System
52285,SRR9077089,SRX5852368,SRS4776361,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,head1 mock,s1,,breed:zebrafish|dev stage:adult|sex:NA|tissue:head1|BioSampleModel:Model organism or animal,,,,,,,,,head1 mock,WC TC 041,WC TC 041,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_041_S8.R1.fastq.gz WC_TC_041_S8.R2.fastq.gz,fastq fastq,5480620528.0,36056714.0,WC TC 041 S8.R1.fastq.gz,0:101 1:51,A:1456079218;C:1286879398;G:1250199115;T:1487095432;N:367365,101,51,,,1456079218,1286879398,1250199115,1487095432,367365,SRX5852368,SRS4776361,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96102,0.95396,0.09057,0.09452,0.70285,0.70573,0.474,0.47396,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Head,Nervous System
52286,SRR9077090,SRX5852367,SRS4776360,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,head1 control,s2,,breed:zebrafish|dev stage:adult|sex:NA|tissue:head2|BioSampleModel:Model organism or animal,,,,,,,,,head1 control,WC TC 042,WC TC 042,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_042_S9.R1.fastq.gz WC_TC_042_S9.R2.fastq.gz,fastq fastq,5011160472.0,32968161.0,WC TC 042 S9.R1.fastq.gz,0:101 1:51,A:1328768028;C:1179737412;G:1141948263;T:1360371072;N:335697,101,51,,,1328768028,1179737412,1141948263,1360371072,335697,SRX5852367,SRS4776360,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.96134,0.95488,0.09183,0.09597,0.70203,0.70398,0.4719,0.46265,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Head,Nervous System
52287,SRR9077091,SRX5852366,SRS4776359,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,head1 kd,s3,,breed:zebrafish|dev stage:adult|sex:NA|tissue:head3|BioSampleModel:Model organism or animal,,,,,,,,,head1 kd,WC TC 043,WC TC 043,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_043_S10.R1.fastq.gz WC_TC_043_S10.R2.fastq.gz,fastq fastq,5709609744.0,37563222.0,WC TC 043 S10.R1.fastq.gz,0:101 1:51,A:1517831332;C:1339538042;G:1299421324;T:1552434811;N:384235,101,51,,,1517831332,1339538042,1299421324,1552434811,384235,SRX5852366,SRS4776359,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.95768,0.95177,0.10352,0.10892,0.69209,0.69556,0.4693,0.47272,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Head,Nervous System
52288,SRR9077092,SRX5852365,SRS4776358,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,head1 kd+wt,s4,,breed:zebrafish|dev stage:adult|sex:NA|tissue:head4|BioSampleModel:Model organism or animal,,,,,,,,,head1 kd+wt,WC TC 044,WC TC 044,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_044_S11.R2.fastq.gz WC_TC_044_S11.R1.fastq.gz,fastq fastq,4776327920.0,31423210.0,WC TC 044 S11.R1.fastq.gz,0:101 1:51,A:1272079335;C:1117051709;G:1087240750;T:1299640784;N:315342,101,51,,,1272079335,1117051709,1087240750,1299640784,315342,SRX5852365,SRS4776358,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.9572,0.95024,0.10519,0.11173,0.69412,0.69621,0.47948,0.46528,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-05-17,Adult,Adult,Head,Nervous System
52292,SRR9077096,SRX5852361,SRS4776354,SRP198708,PRJNA543385,mRNA sequence of zebrafish head and body,PRJNA543385,Other,RNA was isolated from zebrafish head and body separately and followed with standardised Illumina sequencing,,,,head1 kd+mt,s5,,breed:zebrafish|dev stage:adult|sex:NA|tissue:head5|BioSampleModel:Model organism or animal,,,,,,,,,head1 kd+mt,WC TC 045,WC TC 045,TRUEseq standardised protocol,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP198708,,,WC_TC_045_S12.R1.fastq.gz WC_TC_045_S12.R2.fastq.gz,fastq fastq,4914615696.0,32332998.0,WC TC 045 S12.R1.fastq.gz,0:101 1:51,A:1304784949;C:1154087581;G:1119502459;T:1335912697;N:328010,101,51,,,1304784949,1154087581,1119502459,1335912697,328010,SRX5852361,SRS4776354,SRA887738,Southern University of Science and Technology|Department of Biology,Southern University of Science and Technology,2,0.95742,0.95094,0.10146,0.1069,0.69686,0.69978,0.47629,0.469,101,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,China,2019-10-08,Adult,Adult,Head,Nervous System
53640,SRR10004189,SRX6742925,SRS5293748,SRP218844,PRJNA560923,Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a /  and wildtype embryo  head explant,GSE136003,Transcriptome Analysis,This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein  this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant  without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control,,pubmed:32170011,,R 1,GSM4039262,,source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon,R 1,Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt（version 1.9.1） Allignment: Hisat2v2.0.1  default parameter Differential gene expression: DESeq2（V1.6.3） Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file  gene expression level in FPKM Supplementary files format and content: excel file  differentially expressed genes,head explant,the head region of 33 hpf embryos were cut and collected for RNA extraction,Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.,,dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon,GSM4039262,GSM4039262: R 1; Danio rerio; RNA Seq,GSM4039262,,1,Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.,GEO Accession:GSM4039262,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP218844,,,R1_combined_R1.fastq.gz R1_combined_R2.fastq.gz,fastq fastq,7918195500.0,26393985.0,GSM4039262 r1,0:150 1:150,A:2130539253;C:1816469246;G:1847209333;T:2123238120;N:739548,150,150,,,2130539253,1816469246,1847209333,2123238120,739548,SRX6742925,SRS5293748,SRA945259,GEO,"School of Lifesciences, Shandong University",2,0.92358,0.92932,0.06139,0.0616,0.7218,0.73192,0.4833,0.48317,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2019-08-19,Pharyngula,Embryo,Head,Nervous System
53641,SRR10004188,SRX6742924,SRS5293747,SRP218844,PRJNA560923,Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a /  and wildtype embryo  head explant,GSE136003,Transcriptome Analysis,This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein  this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant  without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control,,pubmed:32170011,,WT 1,GSM4039261,,source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB,WT 1,Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt（version 1.9.1） Allignment: Hisat2v2.0.1  default parameter Differential gene expression: DESeq2（V1.6.3） Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file  gene expression level in FPKM Supplementary files format and content: excel file  differentially expressed genes,head explant,the head region of 33 hpf embryos were cut and collected for RNA extraction,Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.,,dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB,GSM4039261,GSM4039261: WT 1; Danio rerio; RNA Seq,GSM4039261,,1,Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.,GEO Accession:GSM4039261,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP218844,,,WT1_combined_R1.fastq.gz WT1_combined_R2.fastq.gz,fastq fastq,6916773600.0,23055912.0,GSM4039261 r1,0:150 1:150,A:1871554357;C:1578397354;G:1603789627;T:1862359143;N:673119,150,150,,,1871554357,1578397354,1603789627,1862359143,673119,SRX6742924,SRS5293747,SRA945259,GEO,"School of Lifesciences, Shandong University",2,0.92052,0.92653,0.07178,0.07144,0.72076,0.73312,0.46318,0.48078,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2019-08-19,Pharyngula,Embryo,Head,Nervous System
59313,SRR11855605,SRX8405706,SRS6718147,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head mt 3,GSM4570141,,source name:Head|strain:AB|tissue:Head|age:36 hpf / ,AB Head mt 3,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf / ,GSM4570141,GSM4570141: AB Head mt 3; Danio rerio; RNA Seq,GSM4570141,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,mt3_2.fastq.gz mt3_1.fastq.gz,fastq fastq,13313574600.0,44378582.0,GSM4570141 r1,0:150 1:150,A:3477543422;C:3199199156;G:3207403563;T:3429195541;N:232918,150,150,,,3477543422,3199199156,3207403563,3429195541,232918,SRX8405706,SRS6718147,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.94266,0.94401,0.08928,0.08979,0.69191,0.69179,0.45995,0.46233,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
59314,SRR11855604,SRX8405705,SRS6718146,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head sib3,GSM4570140,,source name:Head|strain:AB|tissue:Head|age:36 hpf type,AB Head sib3,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf type,GSM4570140,GSM4570140: AB Head sib3; Danio rerio; RNA Seq,GSM4570140,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,sib3_2.fastq.gz sib3_1.fastq.gz,fastq fastq,13010052000.0,43366840.0,GSM4570140 r1,0:150 1:150,A:3375957983;C:3149320854;G:3162958825;T:3321576463;N:237875,150,150,,,3375957983,3149320854,3162958825,3321576463,237875,SRX8405705,SRS6718146,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.95142,0.95014,0.06943,0.06912,0.69049,0.69065,0.45158,0.46064,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
59315,SRR11855603,SRX8405704,SRS6718145,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head mt 2,GSM4570139,,source name:Head|strain:AB|tissue:Head|age:36 hpf / ,AB Head mt 2,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf / ,GSM4570139,GSM4570139: AB Head mt 2; Danio rerio; RNA Seq,GSM4570139,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,mt2_1.fastq.gz mt2_2.fastq.gz,fastq fastq,13374951000.0,44583170.0,GSM4570139 r1,0:150 1:150,A:3463556768;C:3233594067;G:3255830360;T:3421731102;N:238703,150,150,,,3463556768,3233594067,3255830360,3421731102,238703,SRX8405704,SRS6718145,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.94607,0.94512,0.08117,0.08079,0.698,0.69875,0.45364,0.45399,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
59316,SRR11855602,SRX8405703,SRS6718144,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head sib2,GSM4570138,,source name:Head|strain:AB|tissue:Head|age:36 hpf type,AB Head sib2,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf type,GSM4570138,GSM4570138: AB Head sib2; Danio rerio; RNA Seq,GSM4570138,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,sib2_1.fastq.gz sib2_2.fastq.gz,fastq fastq,12076874100.0,40256247.0,GSM4570138 r1,0:150 1:150,A:3116319895;C:2937698203;G:2949917740;T:3072719174;N:219088,150,150,,,3116319895,2937698203,2949917740,3072719174,219088,SRX8405703,SRS6718144,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.95283,0.95237,0.06658,0.06623,0.69292,0.69365,0.44936,0.45234,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
59317,SRR11855601,SRX8405702,SRS6718143,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head mt 1,GSM4570137,,source name:Head|strain:AB|tissue:Head|age:36 hpf / ,AB Head mt 1,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf / ,GSM4570137,GSM4570137: AB Head mt 1; Danio rerio; RNA Seq,GSM4570137,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570137,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,mt1_1.fastq.gz mt1_2.fastq.gz,fastq fastq,12961323900.0,43204413.0,GSM4570137 r1,0:150 1:150,A:3332696255;C:3164828320;G:3171695699;T:3291860380;N:243246,150,150,,,3332696255,3164828320,3171695699,3291860380,243246,SRX8405702,SRS6718143,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.95246,0.94862,0.06807,0.06741,0.71634,0.71585,0.45271,0.44523,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
59318,SRR11855600,SRX8405701,SRS6718142,SRP264942,PRJNA635369,Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing,GSE151273,Transcriptome Analysis,Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis  especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa  a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here  we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level  significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover  genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events  which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 /  zebrafish were generated by deep sequence in three independent biological replicates.,,pubmed:33476374,,AB Head sib1,GSM4570136,,source name:Head|strain:AB|tissue:Head|age:36 hpf type,AB Head sib1,Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene. FPKM  expected number of Fragments Per Kilobase of transcript sequence per  Millions base pairs sequenced  considers the effect of sequencing depth and gene length  for the reads count at the same time  and is currently the most commonly used method for  estimating gene expression levels Trapnell  Cole  et al.  2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample,Head,,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,,strain:AB|tissue:Head|age:36 hpf type,GSM4570136,GSM4570136: AB Head sib1; Danio rerio; RNA Seq,GSM4570136,,1,Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length  the library fragments were purified with AMPure XP system Beckman Coulter  Beverly  USA. Then 3 µl USER Enzyme NEB  USA was used with size selected  adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase  Universal PCR primers and Index X Primer. At last  PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system,GEO Accession:GSM4570136,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP264942,,,sib1_1.fastq.gz sib1_2.fastq.gz,fastq fastq,11694742200.0,38982474.0,GSM4570136 r1,0:150 1:150,A:3017467040;C:2846786828;G:2857204470;T:2973074374;N:209488,150,150,,,3017467040,2846786828,2857204470,2973074374,209488,SRX8405701,SRS6718142,SRA1080304,GEO,Huazhong University of Science and Technology,2,0.95096,0.95068,0.07163,0.07124,0.6939,0.69351,0.46447,0.46482,150,150,B,B,biological fallback assumption,illumina,hiseq_era,5prime,poly_a,nebnext,bulk,unknown,unknown,,China,2020-05-27,Pharyngula,Embryo,Head,Nervous System
61716,SRR13015574,SRX9466662,SRS7678788,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 72hpf head,single cross 2 72hpf head.rep2,,strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos  wildtype AB  72 hpf  head  single cross 2  Rep2  lane2,PJ KH 025 2,PJ KH 025 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_025_S25_L004_R1_001.fastq.gz PJ_KH_025_S25_L004_R2_001.fastq.gz,fastq fastq,6044277226.0,20014163.0,PJ KH 025 S25 L004 R1 001.fastq.gz,0:151 1:151,A:1592897775;C:1431102291;G:1483194415;T:1535949729;N:1133016,151,151,,,1592897775,1431102291,1483194415,1535949729,1133016,SRX9466662,SRS7678788,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.83797,0.8376,0.08415,0.08231,0.67734,0.67984,0.47005,0.47051,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Larval,Larval,Head,Nervous System
61717,SRR13015575,SRX9466661,SRS7678788,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 72hpf head,single cross 2 72hpf head.rep2,,strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos  wildtype AB  72 hpf  head  single cross 2  Rep2  lane1,PJ KH 025 1,PJ KH 025 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_025_S25_L003_R1_001.fastq.gz PJ_KH_025_S25_L003_R2_001.fastq.gz,fastq fastq,5975225530.0,19785515.0,PJ KH 025 S25 L003 R1 001.fastq.gz,0:151 1:151,A:1575693310;C:1413843218;G:1467480556;T:1517391851;N:816595,151,151,,,1575693310,1413843218,1467480556,1517391851,816595,SRX9466661,SRS7678788,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.83685,0.83734,0.08376,0.08206,0.67452,0.67738,0.47208,0.46848,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Larval,Larval,Head,Nervous System
61720,SRR13015578,SRX9466658,SRS7678785,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here  we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw  unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 72hpf head,single cross 2 72hpf head.rep1,,strain:AB wildtype|dev stage:72 hpf|sex:unknown|tissue:head|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos  wildtype AB  72 hpf  head  single cross 2  Rep1  lane2,PJ KH 023 2,PJ KH 023 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_023_S23_L004_R1_001.fastq.gz PJ_KH_023_S23_L004_R2_001.fastq.gz,fastq fastq,6256736038.0,20717669.0,PJ KH 023 S23 L004 R1 001.fastq.gz,0:151 1:151,A:1682521012;C:1447539005;G:1492671488;T:1632844528;N:1160005,151,151,,,1682521012,1447539005,1492671488,1632844528,1160005,SRX9466658,SRS7678785,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94403,0.94422,0.06806,0.06559,0.70849,0.71135,0.4781,0.47695,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Larval,Larval,Head,Nervous System