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
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
11711,ERR11282347,ERX10689990,ERS15395535,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 8,SAMEA113400389,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400389|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 8|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 8|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 8 p,Sample 8 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0008_S1_L005_R2_001.fastq.gz 8680-JP-0008_S1_L005_R1_001.fastq.gz,fastq fastq,21919844332.0,72582266.0,E MTAB 12901:8680 JP 0008 S1 L005 R,0:151 1:151,A:5996325335;C:4770833694;G:5244802952;T:5876120950;N:31761401,151,151,,,5996325335,4770833694,5244802952,5876120950,31761401,ERX10689990,ERS15395535,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92572,0.92425,0.13427,0.13101,0.70086,0.70266,0.50868,0.50381,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11712,ERR11282346,ERX10689989,ERS15395534,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 7,SAMEA113400388,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400388|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 7|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 7|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 7 p,Sample 7 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0007_S1_L005_R2_001.fastq.gz 8680-JP-0007_S1_L005_R1_001.fastq.gz,fastq fastq,20351465316.0,67388958.0,E MTAB 12901:8680 JP 0007 S1 L005 R,0:151 1:151,A:5563989836;C:4461170993;G:4892290448;T:5404916249;N:29097790,151,151,,,5563989836,4461170993,4892290448,5404916249,29097790,ERX10689989,ERS15395534,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.9267,0.9236,0.12782,0.12528,0.70307,0.70473,0.50799,0.50969,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11713,ERR11282345,ERX10689988,ERS15395533,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 6,SAMEA113400387,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400387|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 6|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 6|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 6 p,Sample 6 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0006_S1_L005_R2_001.fastq.gz 8680-JP-0006_S1_L005_R1_001.fastq.gz,fastq fastq,19220102648.0,63642724.0,E MTAB 12901:8680 JP 0006 S1 L005 R,0:151 1:151,A:5250476003;C:4214339559;G:4606611173;T:5120701154;N:27974759,151,151,,,5250476003,4214339559,4606611173,5120701154,27974759,ERX10689988,ERS15395533,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92441,0.92391,0.13718,0.13346,0.70281,0.7024,0.48155,0.49173,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11714,ERR11282344,ERX10689987,ERS15395532,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 3,SAMEA113400386,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400386|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 3|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 3|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 3 p,Sample 3 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0003_S1_L005_R1_001.fastq.gz 8680-JP-0003_S1_L005_R2_001.fastq.gz,fastq fastq,18624364462.0,61670081.0,E MTAB 12901:8680 JP 0003 S1 L005 R,0:151 1:151,A:5114421711;C:4075705896;G:4436341056;T:4970953410;N:26942389,151,151,,,5114421711,4075705896,4436341056,4970953410,26942389,ERX10689987,ERS15395532,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92553,0.92378,0.13069,0.12709,0.69988,0.70258,0.4969,0.51157,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11715,ERR11282343,ERX10689986,ERS15395531,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 2,SAMEA113400385,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400385|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 2|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 2|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 2 p,Sample 2 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0002_S1_L005_R1_001.fastq.gz 8680-JP-0002_S1_L005_R2_001.fastq.gz,fastq fastq,15153807038.0,50178169.0,E MTAB 12901:8680 JP 0002 S1 L005 R,0:151 1:151,A:4156183785;C:3309476575;G:3635942314;T:4030261947;N:21942417,151,151,,,4156183785,3309476575,3635942314,4030261947,21942417,ERX10689986,ERS15395531,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92069,0.91964,0.13733,0.13466,0.70102,0.70185,0.48507,0.48992,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11716,ERR11282342,ERX10689985,ERS15395530,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 1,SAMEA113400384,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400384|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 1|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|organism part:brain|sample name:E MTAB 12901:Sample 1|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 1 p,Sample 1 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0001_S1_L005_R2_001.fastq.gz 8680-JP-0001_S1_L005_R1_001.fastq.gz,fastq fastq,17758550696.0,58803148.0,E MTAB 12901:8680 JP 0001 S1 L005 R,0:151 1:151,A:4866917250;C:3906782394;G:4241519777;T:4717566830;N:25764445,151,151,,,4866917250,3906782394,4241519777,4717566830,25764445,ERX10689985,ERS15395530,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92263,0.92154,0.13341,0.12969,0.69443,0.69658,0.48648,0.49678,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11717,ERR11282341,ERX10689984,ERS15395529,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 9,SAMEA113400383,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400383|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 9|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 9|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 9 p,Sample 9 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0009_S1_L005_R2_001.fastq.gz 8680-JP-0009_S1_L005_R1_001.fastq.gz,fastq fastq,21619735456.0,71588528.0,E MTAB 12901:8680 JP 0009 S1 L005 R,0:151 1:151,A:5904040180;C:4720941204;G:5229712921;T:5733559571;N:31481580,151,151,,,5904040180,4720941204,5229712921,5733559571,31481580,ERX10689984,ERS15395529,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92235,0.92126,0.13956,0.13682,0.70378,0.70526,0.4929,0.49286,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11718,ERR11282340,ERX10689983,ERS15395528,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 11,SAMEA113400382,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400382|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 11|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 11|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 11 p,Sample 11 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0011_S1_L005_R1_001.fastq.gz 8680-JP-0011_S1_L005_R2_001.fastq.gz,fastq fastq,20372991574.0,67460237.0,E MTAB 12901:8680 JP 0011 S1 L005 R,0:151 1:151,A:5569250549;C:4448986210;G:4925237941;T:5399892024;N:29624850,151,151,,,5569250549,4448986210,4925237941,5399892024,29624850,ERX10689983,ERS15395528,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92578,0.92449,0.12979,0.12632,0.69666,0.69775,0.51379,0.51557,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11719,ERR11282339,ERX10689982,ERS15395527,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 10,SAMEA113400381,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400381|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 10|age:2|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 10|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 10 p,Sample 10 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0010_S1_L005_R1_001.fastq.gz 8680-JP-0010_S1_L005_R2_001.fastq.gz,fastq fastq,21517298566.0,71249333.0,E MTAB 12901:8680 JP 0010 S1 L005 R,0:151 1:151,A:5890133399;C:4693794003;G:5193013881;T:5709021540;N:31335743,151,151,,,5890133399,4693794003,5193013881,5709021540,31335743,ERX10689982,ERS15395527,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92431,0.92248,0.13476,0.13116,0.70203,0.70283,0.50087,0.50123,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11720,ERR11282338,ERX10689981,ERS15395526,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 5,SAMEA113400380,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400380|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 5|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 5|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 5 p,Sample 5 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0005_S1_L005_R1_001.fastq.gz 8680-JP-0005_S1_L005_R2_001.fastq.gz,fastq fastq,25670665306.0,85002203.0,E MTAB 12901:8680 JP 0005 S1 L005 R,0:151 1:151,A:7004508034;C:5563021332;G:6252648683;T:6813680645;N:36806612,151,151,,,7004508034,5563021332,6252648683,6813680645,36806612,ERX10689981,ERS15395526,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92268,0.92095,0.13119,0.12796,0.70234,0.70276,0.51658,0.51519,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11721,ERR11282337,ERX10689980,ERS15395525,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 4,SAMEA113400379,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400379|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 4|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 4|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 4 p,Sample 4 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0004_S1_L005_R1_001.fastq.gz 8680-JP-0004_S1_L005_R2_001.fastq.gz,fastq fastq,19678467074.0,65160487.0,E MTAB 12901:8680 JP 0004 S1 L005 R,0:151 1:151,A:5388172969;C:4290008191;G:4741082570;T:5230699181;N:28504163,151,151,,,5388172969,4290008191,4741082570,5230699181,28504163,ERX10689980,ERS15395525,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92019,0.91807,0.13779,0.13325,0.69739,0.69682,0.48956,0.48353,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11722,ERR11282336,ERX10689979,ERS15395524,ERP146895,PRJEB61813,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E-MTAB-12901,Other,The ATP binding cassette subfamily B member 1 ABCB1  encoding a multidrug transporter P glycoprotein  plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy—however  little information regarding Pgp at the zebrafish. In addition  to study the function of Pgp in the zebrafish brain in the aging process  we performed RNA seq using brain tissue of WT and abcb4 knockout zebrafish at different ages  such as 2 month and 30 month.,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,,Protocols: brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Sample 12,SAMEA113400378,VANDERBILT UNIVERSITY,ENA FIRST PUBLIC:2023 07 14T00:23:41Z|ENA LAST UPDATE:2023 07 14T00:23:41Z|External Id:SAMEA113400378|INSDC center alias:VANDERBILT UNIVERSITY|INSDC center name:VANDERBILT UNIVERSITY|INSDC first public:2023 07 14T00:23:41Z|INSDC last update:2023 07 14T00:23:41Z|INSDC status:public|Submitter Id:E MTAB 12901:Sample 12|age:30|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:abcb4  / |organism part:brain|sample name:E MTAB 12901:Sample 12|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,E MTAB 12901:Sample 12 p,Sample 12 p,RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,brain tissue were dissected from zebrafish and snap frozen until RNA isolation Trizol + zymo RNA clean column kit TruSeq RNA sample prep kit Illumina to prepare cDNA libraries post PolyA selection,Experimental Factor: genotype:abcb4  / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP146895,Illumina NovaSeq 6000 paired end sequencing; RNA seq of brain tissues of WT and abcb4 knockout zebrafish at 2 month and 30 month,ENA FIRST PUBLIC:2023 07 14|ENA LAST UPDATE:2023 07 14,8680-JP-0012_S1_L005_R1_001.fastq.gz 8680-JP-0012_S1_L005_R2_001.fastq.gz,fastq fastq,19025354324.0,62997862.0,E MTAB 12901:8680 JP 0012 S1 L005 R,0:151 1:151,A:5203524540;C:4195830684;G:4551047863;T:5047420365;N:27530872,151,151,,,5203524540,4195830684,4551047863,5047420365,27530872,ERX10689979,ERS15395524,ERA23235100,VANDERBILT UNIVERSITY|European Nucleotide Archive,VANDERBILT UNIVERSITY|European Nucleotide Archive,2,0.92091,0.92095,0.13145,0.12737,0.69238,0.69258,0.50372,0.48431,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2023-07-14,Adult,Adult,Brain,Nervous System
11813,ERR11788863,ERX11187331,ERS16221143,ERP149944,PRJEB64780,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E-MTAB-13223,Transcriptome Analysis,To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes  using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina,Sample 1,SAMEA114235870,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E MTAB 13223:Sample 1 p,Sample 1 p,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  RNA Illumina,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP149944,NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,L41805_Track-81843_R1.fastq.gz L41805_Track-81843_R2.fastq.gz,fastq fastq,5545444464.0,66017196.0,E MTAB 13223:L41805 Track 81843,0:28 1:56,A:1576174024;C:1193175858;G:1221776615;T:1551009004;N:3308963,28,56,,,1576174024,1193175858,1221776615,1551009004,3308963,ERX11187331,ERS16221143,ERA26318932,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.00738,0.90151,0.00285,0.20553,0.99072,0.82402,0.4645,0.53817,28,56,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
11814,ERR11788864,ERX11187331,ERS16221143,ERP149944,PRJEB64780,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E-MTAB-13223,Transcriptome Analysis,To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes  using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,,Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina,Sample 1,SAMEA114235870,Universite Libre de Bruxelles,ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB,,,,,,,,,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,E MTAB 13223:Sample 1 p,Sample 1 p,A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1µM  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  RNA Illumina,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP149944,NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain,ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25,L41805_Track-81377_R1.fastq.gz L41805_Track-81377_R2.fastq.gz,fastq fastq,3184137096.0,37906394.0,E MTAB 13223:L41805 Track 81377,0:28 1:56,A:899943184;C:685571078;G:703849582;T:889228559;N:5544693,28,56,,,899943184,685571078,703849582,889228559,5544693,ERX11187331,ERS16221143,ERA26318932,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,2,0.00734,0.90077,0.00293,0.20318,0.99064,0.82765,0.47994,0.53473,28,56,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-12-25,Adult,Adult,Brain,Nervous System
31902,SRR28763293,SRX24328715,SRS21090019,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB19,,replicate name:10|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB19,EB19,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB19_1.fastq.gz EB19_2.fastq.gz,fastq fastq,9436386526.0,31246313.0,EB19 1.fastq.gz,0:151 1:151,A:2716315062;C:1976294752;G:2147671436;T:2595980360;N:124916,151,151,,,2716315062,1976294752,2147671436,2595980360,124916,SRX24328715,SRS21090019,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.91409,0.91345,0.24896,0.24788,0.78056,0.78279,0.72332,0.73168,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31903,SRR28763294,SRX24328714,SRS21090018,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB18,,replicate name:9|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB18,EB18,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB18_1.fastq.gz EB18_2.fastq.gz,fastq fastq,9118420390.0,30193445.0,EB18 1.fastq.gz,0:151 1:151,A:2629035452;C:1916588061;G:2003273132;T:2569401842;N:121903,151,151,,,2629035452,1916588061,2003273132,2569401842,121903,SRX24328714,SRS21090018,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92136,0.91989,0.22403,0.22513,0.72318,0.72344,0.58479,0.59137,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31904,SRR28763295,SRX24328713,SRS21090017,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB13,,replicate name:8|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB13,EB13,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB13_1.fastq.gz EB13_2.fastq.gz,fastq fastq,9079809388.0,30065594.0,EB13 1.fastq.gz,0:151 1:151,A:2664300477;C:1849456779;G:1954969464;T:2610962453;N:120215,151,151,,,2664300477,1849456779,1954969464,2610962453,120215,SRX24328713,SRS21090017,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92157,0.92274,0.20709,0.20463,0.77609,0.77962,0.77474,0.76073,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31905,SRR28763296,SRX24328712,SRS21090016,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB11,,replicate name:7|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB11,EB11,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB11_1.fastq.gz EB11_2.fastq.gz,fastq fastq,9504832712.0,31472956.0,EB11 1.fastq.gz,0:151 1:151,A:2795532595;C:1925063954;G:2051665162;T:2732443741;N:127260,151,151,,,2795532595,1925063954,2051665162,2732443741,127260,SRX24328712,SRS21090016,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.93395,0.93446,0.15772,0.15556,0.87117,0.87462,0.89532,0.89681,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31906,SRR28763297,SRX24328711,SRS21090015,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB10,,replicate name:6|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 08|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB10,EB10,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB10_1.fastq.gz EB10_2.fastq.gz,fastq fastq,9789274734.0,32414817.0,EB10 1.fastq.gz,0:151 1:151,A:2824956587;C:2042095073;G:2194234020;T:2727859573;N:129481,151,151,,,2824956587,2042095073,2194234020,2727859573,129481,SRX24328711,SRS21090015,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92285,0.9232,0.22353,0.22316,0.76658,0.76723,0.70407,0.36056,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31907,SRR28763298,SRX24328710,SRS21090014,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB7,,replicate name:5|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB7,EB7,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB7_1.fastq.gz EB7_2.fastq.gz,fastq fastq,10834721120.0,35876560.0,EB7 1.fastq.gz,0:151 1:151,A:3080234341;C:2317625501;G:2459979119;T:2976734982;N:147177,151,151,,,3080234341,2317625501,2459979119,2976734982,147177,SRX24328710,SRS21090014,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.91597,0.91208,0.20246,0.20371,0.70711,0.70737,0.46676,0.54014,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31908,SRR28763299,SRX24328709,SRS21090013,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB6,,replicate name:4|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB6,EB6,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB6_1.fastq.gz EB6_2.fastq.gz,fastq fastq,9741721512.0,32257356.0,EB6 1.fastq.gz,0:151 1:151,A:2786663368;C:2058810098;G:2182236675;T:2713885545;N:125826,151,151,,,2786663368,2058810098,2182236675,2713885545,125826,SRX24328709,SRS21090013,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.9221,0.91676,0.20096,0.20109,0.71885,0.72109,0.5729,0.56637,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31915,SRR28763306,SRX24328702,SRS21090006,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB5,,replicate name:3|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB5,EB5,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB5_1.fastq.gz EB5_2.fastq.gz,fastq fastq,10009088756.0,33142678.0,EB5 1.fastq.gz,0:151 1:151,A:2928623095;C:2061836360;G:2174039537;T:2844456450;N:133314,151,151,,,2928623095,2061836360,2174039537,2844456450,133314,SRX24328702,SRS21090006,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.9185,0.91663,0.21613,0.21748,0.71829,0.71967,0.56772,0.56625,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31922,SRR28763313,SRX24328695,SRS21089999,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB27,,replicate name:14|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB27,EB27,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB27_1.fastq.gz EB27_2.fastq.gz,fastq fastq,9161773094.0,30336997.0,EB27 1.fastq.gz,0:151 1:151,A:2605950329;C:1969811465;G:2071575244;T:2514313551;N:122505,151,151,,,2605950329,1969811465,2071575244,2514313551,122505,SRX24328695,SRS21089999,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92523,0.92363,0.21064,0.21169,0.70964,0.70991,0.55438,0.55426,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31923,SRR28763314,SRX24328694,SRS21089998,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB26,,replicate name:13|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB26,EB26,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB26_1.fastq.gz EB26_2.fastq.gz,fastq fastq,9240227560.0,30596780.0,EB26 1.fastq.gz,0:151 1:151,A:2642944689;C:1958167494;G:2078976911;T:2560016979;N:121487,151,151,,,2642944689,1958167494,2078976911,2560016979,121487,SRX24328694,SRS21089998,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92264,0.92192,0.21746,0.21734,0.73292,0.73383,0.62606,0.61636,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31924,SRR28763315,SRX24328693,SRS21089997,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB25,,replicate name:12|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB25,EB25,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB25_1.fastq.gz EB25_2.fastq.gz,fastq fastq,9625587110.0,31872805.0,EB25 1.fastq.gz,0:151 1:151,A:2795560694;C:1995787311;G:2099611038;T:2734501492;N:126575,151,151,,,2795560694,1995787311,2099611038,2734501492,126575,SRX24328693,SRS21089997,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92658,0.92669,0.20737,0.20889,0.74637,0.74852,0.665,0.67094,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31925,SRR28763316,SRX24328692,SRS21089996,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB21,,replicate name:11|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 14|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB21,EB21,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB21_1.fastq.gz EB21_2.fastq.gz,fastq fastq,9252105220.0,30636110.0,EB21 1.fastq.gz,0:151 1:151,A:2713520368;C:1892341723;G:1978899105;T:2667222416;N:121608,151,151,,,2713520368,1892341723,1978899105,2667222416,121608,SRX24328692,SRS21089996,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92204,0.92307,0.20614,0.20487,0.77561,0.77956,0.75506,0.73666,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31926,SRR28763317,SRX24328691,SRS21089995,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB4,,replicate name:2|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB4,EB4,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB4_1.fastq.gz EB4_2.fastq.gz,fastq fastq,10173670300.0,33687650.0,EB4 1.fastq.gz,0:151 1:151,A:2946513536;C:2116612054;G:2242572059;T:2867836703;N:135948,151,151,,,2946513536,2116612054,2242572059,2867836703,135948,SRX24328691,SRS21089995,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92771,0.92647,0.2039,0.20424,0.74485,0.74679,0.67237,0.67051,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
31927,SRR28763318,SRX24328690,SRS21089994,SRP503258,PRJNA1102381,Acidification alters anxiety like behaviour and brain gene expression in zebrafish,PRJNA1102381,Other,CO2 driven acidification of freshwater ecosystems is an accelerating process that can impact aquatic life in the future. Despite their importance in accurately predicting how future freshwater teleost fish will respond to changing environments  molecular mechanisms coordinating the response to elevated CO2 have not been extensively studied. Making use of the zebrafish Danio rerio considered 'tolerant' to acidified waters  we analyzed the behavioural and transcriptomic response to acidification to highlight potential response mechanisms in the brain and the gills which mediate behaviour and perform acid base regulation. Adult zebrafish were exposed to control 500 uatm and elevated CO2 1000 uatm for five days and submitted to Open Field and Novel Object Approach tests  revealing a decrease in anxiety like behaviour in response to elevated CO2. In the brain  acidification caused differential expression of genes involved in cytoskeletal organization  cellular transport  immunity and the visual neural system. In the gills  an elevated expression of genes involved in immune response and oxidoreduction with increasing pCO2 in combination with decreased anxiety like behaviour point to an increase of oxidative stress. However  the absence of differentially expressed genes in gills indicates that this species has adapted to regulating its acid base balance in acidified waters  common in its natural habitat. Our study pinpoints the molecular response to elevated CO2 possibly triggering behavioural changes in zebrafish and suggest that not only marine  but also freshwater fishes will be behaviourally affected by acidification due to rapid climate change.,,,,,EB3,,replicate name:1|breed:AB|age:4 months|dev stage:adult|collection date:2021 11 02|geo loc name:Hong Kong|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of 4mpf Danio rerio brain,EB3,EB3,Total RNA was extracted using the RNeasy Micro Kit Qiagen.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503258,,,EB3_1.fastq.gz EB3_2.fastq.gz,fastq fastq,9627538030.0,31879265.0,EB3 1.fastq.gz,0:151 1:151,A:2735805884;C:2063838700;G:2168523582;T:2659242105;N:127759,151,151,,,2735805884,2063838700,2168523582,2659242105,127759,SRX24328690,SRS21089994,SRA1849282,The University of Hong Kong|School of Biological Sciences,The University of Hong Kong,2,0.92558,0.92158,0.18877,0.18982,0.71752,0.71865,0.57954,0.58018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-22,Adult,Adult,Brain,Nervous System
34192,SRR31443228,SRX26812023,SRS23296672,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 3,srrm4[y712] mutant replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut3.pass2Aligned.sortedByCoord.out.bam,bam,23466336192.0,117587529.0,25938 mut3.pass2Aligned.sortedByCoord.out.bam,0:100.13 1:100.08,A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927,100,100,,,6298034402,5433884683,5344985734,6388443446,987927,SRX26812023,SRS23296672,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95864,0.95894,0.10681,0.1052,0.65385,0.65403,0.46511,0.46252,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34193,SRR31443229,SRX26812022,SRS23296671,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 3,srrm4[y712] wild type replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt3.pass2Aligned.sortedByCoord.out.bam,bam,23979171134.0,120156039.0,25938 wt3.pass2Aligned.sortedByCoord.out.bam,0:100.12 1:100.07,A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857,100,100,,,6398807397,5589997524,5503127729,6486232627,1005857,SRX26812022,SRS23296671,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95941,0.96004,0.10323,0.10191,0.65451,0.6532,0.46396,0.46398,101,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34194,SRR31443230,SRX26812021,SRS23296670,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 2,srrm4[y712] mutant replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut2.pass2Aligned.sortedByCoord.out.bam,bam,20256127500.0,101792067.0,25938 mut2.pass2Aligned.sortedByCoord.out.bam,0:100.05 1:100.00,A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366,100,100,,,5435798119,4683997479,4650293108,5485187428,851366,SRX26812021,SRS23296670,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96008,0.96049,0.10232,0.10156,0.66072,0.65932,0.4668,0.46817,95,95,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34195,SRR31443231,SRX26812020,SRS23296669,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 2,srrm4[y712] wild type replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt2.pass2Aligned.sortedByCoord.out.bam,bam,22698373371.0,113599687.0,25938 wt2.pass2Aligned.sortedByCoord.out.bam,0:100.18 1:100.12,A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128,100,100,,,6063922145,5275724786,5212055837,6145709475,961128,SRX26812020,SRS23296669,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96129,0.96063,0.1003,0.09861,0.65744,0.65748,0.46167,0.46817,98,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34196,SRR31443232,SRX26812019,SRS23296667,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 1,srrm4[y712] mutant replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut.pass2Aligned.sortedByCoord.out.bam,bam,11282501509.0,56702666.0,25938 mut.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.55,A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849,99,99,,,2764745971,2868447715,2856237429,2792914545,155849,SRX26812019,SRS23296667,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34197,SRR31443233,SRX26812018,SRS23296668,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 1,srrm4[y712] wild type replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt.pass2Aligned.sortedByCoord.out.bam,bam,16346812838.0,82104499.0,25938 wt.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.56,A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992,99,99,,,3996717287,4167381503,4130586142,4051899914,227992,SRX26812018,SRS23296668,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.97776,0.97907,0.04095,0.04006,0.6702,0.67034,0.46611,0.46144,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
35865,SRR33094447,SRX28358130,SRS24687221,SRP578075,PRJNA1249535,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,PRJNA1249535,Other,Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish  providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.,,,TauP301S 4,,TauP301S 4,,breed:zebrafish|age:4 month|collection date:2024 05 18|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,TauP301S 4,TauP301S 4,tissue,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,BGISEQ,BGISEQ-500,,SRP578075,,,AD4_S1_L001_R1_001.fastq.gz AD4_S1_L001_R2_001.fastq.gz,fastq fastq,129145897746.0,427635423.0,AD4 S1 L001 R1 001.fastq.gz,0:151 1:151,A:37870495722;C:24917123133;G:22536537853;T:43764941649;N:56799389,151,151,,,37870495722,24917123133,22536537853,43764941649,56799389,SRX28358130,SRS24687221,SRA2110625,Shantou university medical college|Neuroscience Center,Shantou university medical college,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,sc,unknown,unknown,,China,2025-04-13,Adult,Adult,Brain,Nervous System
35866,SRR33094448,SRX28358129,SRS24687220,SRP578075,PRJNA1249535,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,PRJNA1249535,Other,Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish  providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.,,,TauP301S 3,,TauP301S 3,,breed:zebrafish|age:4 month|collection date:2024 05 17|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,TauP301S 3,TauP301S 3,tissue,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,BGISEQ,BGISEQ-500,,SRP578075,,,AD3_S1_L001_R1_001.fastq.gz AD3_S1_L001_R2_001.fastq.gz,fastq fastq,130723873718.0,432860509.0,AD3 S1 L001 R1 001.fastq.gz,0:151 1:151,A:38509426012;C:25238065771;G:22586405501;T:44332442791;N:57533643,151,151,,,38509426012,25238065771,22586405501,44332442791,57533643,SRX28358129,SRS24687220,SRA2110625,Shantou university medical college|Neuroscience Center,Shantou university medical college,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,sc,unknown,unknown,,China,2025-04-13,Adult,Adult,Brain,Nervous System
35867,SRR33094449,SRX28358128,SRS24687219,SRP578075,PRJNA1249535,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,PRJNA1249535,Other,Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish  providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.,,,TauP301S 2,,TauP301S 2,,breed:zebrafish|age:4 month|collection date:2024 05 16|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,TauP301S 2,TauP301S 2,tissue,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,BGISEQ,BGISEQ-500,,SRP578075,,,AD2_S1_L001_R1_001.fastq.gz AD2_S1_L001_R2_001.fastq.gz,fastq fastq,130145208498.0,430944399.0,AD2 S1 L001 R1 001.fastq.gz,0:151 1:151,A:37802929660;C:22980541562;G:20982421471;T:48304142442;N:75173363,151,151,,,37802929660,22980541562,20982421471,48304142442,75173363,SRX28358128,SRS24687219,SRA2110625,Shantou university medical college|Neuroscience Center,Shantou university medical college,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,sc,unknown,unknown,,China,2025-04-13,Adult,Adult,Brain,Nervous System
35868,SRR33094450,SRX28358127,SRS24687218,SRP578075,PRJNA1249535,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,PRJNA1249535,Other,Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish  providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.,,,TauP301S 1,,TauP301S 1,,breed:zebrafish|age:4 month|collection date:2024 05 15|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy,TauP301S 1,TauP301S 1,tissue,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,BGISEQ,BGISEQ-500,,SRP578075,,,AD1_S1_L001_R1_001.fastq.gz AD1_S1_L001_R2_001.fastq.gz,fastq fastq,151897861402.0,502973051.0,AD1 S1 L001 R1 001.fastq.gz,0:151 1:151,A:44290580650;C:26864167508;G:24611898618;T:56043760812;N:87453814,151,151,,,44290580650,26864167508,24611898618,56043760812,87453814,SRX28358127,SRS24687218,SRA2110625,Shantou university medical college|Neuroscience Center,Shantou university medical college,,,,,,,,,,,,T,B,mate1 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,sc,unknown,unknown,,China,2025-04-13,Adult,Adult,Brain,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
68349,SRR17714692,SRX13877717,SRS11747891,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,WT br 4,,strain:AB type|isolate:wild type|breed:WT br 4|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,WT br 4,WT br 4,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_WT-br-4_good_1.fq.gz Daniorerio_WT-br-4_good_2.fq.gz,fastq fastq,7496868324.0,25083735.0,Daniorerio WT br 4 good 1.fq.gz,0:149.44 1:149.44,A:2075060953;C:1661290867;G:1697443641;T:2062703710;N:369153,149,149,,,2075060953,1661290867,1697443641,2062703710,369153,SRX13877717,SRS11747891,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.92105,0.9212,0.17618,0.17502,0.68844,0.69035,0.48965,0.48899,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68350,SRR17714693,SRX13877716,SRS11747889,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,WT br 3,,strain:AB type|isolate:wild type|breed:WT br 3|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,WT br 3,WT br 3,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_WT-br-3_good_1.fq.gz Daniorerio_WT-br-3_good_2.fq.gz,fastq fastq,6073470194.0,20313710.0,Daniorerio WT br 3 good 1.fq.gz,0:149.49 1:149.49,A:1713896651;C:1313013182;G:1348015489;T:1698243797;N:301075,149,149,,,1713896651,1313013182,1348015489,1698243797,301075,SRX13877716,SRS11747889,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91892,0.91619,0.18079,0.17925,0.68864,0.69039,0.49157,0.48629,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68351,SRR17714694,SRX13877715,SRS11747887,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,WT br 2,,strain:AB type|isolate:wild type|breed:WT br 2|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,WT br 2,WT br 2,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_WT-br-2_good_1.fq.gz Daniorerio_WT-br-2_good_2.fq.gz,fastq fastq,6877930220.0,23036331.0,Daniorerio WT br 2 good 1.fq.gz,0:149.28 1:149.28,A:1905660754;C:1522223390;G:1554569711;T:1895137309;N:339056,149,149,,,1905660754,1522223390,1554569711,1895137309,339056,SRX13877715,SRS11747887,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.9194,0.919,0.17062,0.16948,0.69408,0.69501,0.49041,0.46872,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68352,SRR17714695,SRX13877714,SRS11747888,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,WT br 1,,strain:AB type|isolate:wild type|breed:WT br 1|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,WT br 1,WT br 1,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_WT-br-1_good_1.fq.gz Daniorerio_WT-br-1_good_2.fq.gz,fastq fastq,6677275476.0,22349958.0,Daniorerio WT br 1 good 1.fq.gz,0:149.38 1:149.38,A:1851526469;C:1477465442;G:1505977213;T:1841977322;N:329030,149,149,,,1851526469,1477465442,1505977213,1841977322,329030,SRX13877714,SRS11747888,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91982,0.9189,0.16897,0.16834,0.69631,0.69802,0.48999,0.49186,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68355,SRR17714698,SRX13877711,SRS11747883,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,KO br 4,,strain:AB type|isolate:knockout|breed:KO br 4|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,KO br 4,KO br 4,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_KO-br-4_good_1.fq.gz Daniorerio_KO-br-4_good_2.fq.gz,fastq fastq,7447389410.0,24933883.0,Daniorerio KO br 4 good 1.fq.gz,0:149.34 1:149.34,A:2068669098;C:1645485987;G:1683682550;T:2049528614;N:23161,149,149,,,2068669098,1645485987,1683682550,2049528614,23161,SRX13877711,SRS11747883,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91528,0.91474,0.16702,0.16723,0.69004,0.69132,0.48334,0.48557,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68366,SRR17714709,SRX13877700,SRS11747872,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,KO br 3,,strain:AB type|isolate:knockout|breed:KO br 3|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,KO br 3,KO br 3,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_KO-br-3_good_1.fq.gz Daniorerio_KO-br-3_good_2.fq.gz,fastq fastq,7677925588.0,25687375.0,Daniorerio KO br 3 good 1.fq.gz,0:149.45 1:149.45,A:2141293019;C:1686478627;G:1724464315;T:2125665018;N:24609,149,149,,,2141293019,1686478627,1724464315,2125665018,24609,SRX13877700,SRS11747872,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.9154,0.91488,0.17232,0.17035,0.69227,0.69449,0.47379,0.48628,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68367,SRR17714710,SRX13877699,SRS11747873,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,MU br 4,,strain:AB type|isolate:point mutation|breed:MU br 4|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,MU br 4,MU br 4,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_MU-br-4_good_1.fq.gz Daniorerio_MU-br-4_good_2.fq.gz,fastq fastq,7375252226.0,24699759.0,Daniorerio MU br 4 good 1.fq.gz,0:149.30 1:149.30,A:2085033695;C:1591116585;G:1620970196;T:2077764269;N:367481,149,149,,,2085033695,1591116585,1620970196,2077764269,367481,SRX13877699,SRS11747873,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.911,0.90829,0.19059,0.18896,0.6842,0.68592,0.49423,0.49913,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68368,SRR17714711,SRX13877698,SRS11747871,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,MU br 3,,strain:AB type|isolate:point mutation|breed:MU br 3|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,MU br 3,MU br 3,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_MU-br-3_good_1.fq.gz Daniorerio_MU-br-3_good_2.fq.gz,fastq fastq,8829806410.0,29560399.0,Daniorerio MU br 3 good 1.fq.gz,0:149.35 1:149.35,A:2496211455;C:1905517808;G:1942497707;T:2485137146;N:442294,149,149,,,2496211455,1905517808,1942497707,2485137146,442294,SRX13877698,SRS11747871,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91669,0.91532,0.19181,0.19077,0.69568,0.69589,0.48604,0.48561,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68369,SRR17714712,SRX13877697,SRS11747869,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,MU br 2,,strain:AB type|isolate:point mutation|breed:MU br 2|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,MU br 2,MU br 2,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_MU-br-2_good_1.fq.gz Daniorerio_MU-br-2_good_2.fq.gz,fastq fastq,7338057954.0,24598168.0,Daniorerio MU br 2 good 1.fq.gz,0:149.16 1:149.16,A:2058068771;C:1600708765;G:1631740601;T:2047172313;N:367504,149,149,,,2058068771,1600708765,1631740601,2047172313,367504,SRX13877697,SRS11747869,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91566,0.91378,0.18522,0.18394,0.69201,0.69236,0.4969,0.49242,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68370,SRR17714713,SRX13877696,SRS11747870,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,MU br 1,,strain:AB type|isolate:point mutation|breed:MU br 1|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,MU br 1,MU br 1,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_MU-br-1_good_1.fq.gz Daniorerio_MU-br-1_good_2.fq.gz,fastq fastq,8217544426.0,27571297.0,Daniorerio MU br 1 good 1.fq.gz,0:149.02 1:149.02,A:2292077990;C:1805071065;G:1840323909;T:2279661276;N:410186,149,149,,,2292077990,1805071065,1840323909,2279661276,410186,SRX13877696,SRS11747870,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91869,0.91663,0.1747,0.17413,0.69369,0.69479,0.46987,0.47898,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68377,SRR17714720,SRX13877689,SRS11747861,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,KO br 2,,strain:AB type|isolate:knockout|breed:KO br 2|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,KO br 2,KO br 2,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_KO-br-2_good_1.fq.gz Daniorerio_KO-br-2_good_2.fq.gz,fastq fastq,6926366374.0,23168782.0,Daniorerio KO br 2 good 1.fq.gz,0:149.48 1:149.48,A:1935071993;C:1518964140;G:1551567622;T:1920740127;N:22492,149,149,,,1935071993,1518964140,1551567622,1920740127,22492,SRX13877689,SRS11747861,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.91501,0.91449,0.16712,0.16608,0.68927,0.68974,0.49324,0.4917,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
68378,SRR17714721,SRX13877688,SRS11747862,SRP356388,PRJNA799842,RNA seq of CRISPR/Cas9 mediated genome editing zebrafishes; the alligator pipefish spleen and the small white organ of the lined seahorse.,PRJNA799842,Other,To explore the function of the gene in spleen development  we generated a knockout zebrafish line. To investigate whether the phenotypic consequences in the seahorses were caused by a missense mutation in this gene  we generated a point mutation zebrafish line by CRISPR/Cas9 mediated homologous recombination HR. RNA seq of these samples tissues brain  liver  kidney  and intestine were analyzed. In addition  to clarify the splenic phenotype of the Syngnathidaes  the transcriptomic profiles of the S. biaculeatus spleens and the H. erectus small white organ were also sampled and sequenced.,,,,,KO br 1,,strain:AB type|isolate:knockout|breed:KO br 1|age:3 month|dev stage:NA|sex:NA|tissue:brain|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,KO br 1,KO br 1,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP356388,,loader:fastq load.py,Daniorerio_KO-br-1_good_1.fq.gz Daniorerio_KO-br-1_good_2.fq.gz,fastq fastq,8695204456.0,29088179.0,Daniorerio KO br 1 good 1.fq.gz,0:149.46 1:149.46,A:2427675374;C:1907757731;G:1949179978;T:2410564055;N:27318,149,149,,,2427675374,1907757731,1949179978,2410564055,27318,SRX13877688,SRS11747862,SRA1360632,South China Sea Institute of Oceanology|CAS Key Laboratory of Tropical Marine Bio-Resource,South China Sea Institute of Oceanology,2,0.9149,0.91459,0.16735,0.1673,0.68954,0.69023,0.49497,0.49633,116,116,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-01-27,Adult,Adult,Brain,Nervous System
70109,SRR19561929,SRX15614021,SRS13314715,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 3,Dr13 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 54 13 3 Brain,54 13 3 Brain,54 13 3 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6053 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,54-13-3-Brain-RNA_R1.fq.gz 54-13-3-Brain-RNA_R2.fq.gz,fastq fastq,8519592000.0,28398640.0,54 13 3 Brain RNA R1.fq.gz,0:150 1:150,A:2380407110;C:1852161157;G:1886481748;T:2400379887;N:162098,150,150,,,2380407110,1852161157,1886481748,2400379887,162098,SRX15614021,SRS13314715,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92362,0.924,0.15682,0.15728,0.70926,0.71394,0.49285,0.50156,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70113,SRR19561933,SRX15614017,SRS13314707,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 1,Dr27 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 46 27 1 Brain,46 27 1 Brain,46 27 1 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6005 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,46-27-1-Brain-RNA_R1.fq.gz 46-27-1-Brain-RNA_R2.fq.gz,fastq fastq,6987525300.0,23291751.0,46 27 1 Brain RNA R1.fq.gz,0:150 1:150,A:2005854815;C:1466721021;G:1498208671;T:2016609597;N:131196,150,150,,,2005854815,1466721021,1498208671,2016609597,131196,SRX15614017,SRS13314707,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.9217,0.92302,0.16019,0.15936,0.7218,0.72665,0.51402,0.49955,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70116,SRR19561936,SRX15614014,SRS13314714,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 2,Dr13 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 53 13 2 Brain,53 13 2 Brain,53 13 2 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6047 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,53-13-2-Brain-RNA_R1.fq.gz 53-13-2-Brain-RNA_R2.fq.gz,fastq fastq,7058502300.0,23528341.0,53 13 2 Brain RNA R1.fq.gz,0:150 1:150,A:1992967170;C:1514239722;G:1545290515;T:2005873325;N:131568,150,150,,,1992967170,1514239722,1545290515,2005873325,131568,SRX15614014,SRS13314714,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92235,0.92276,0.16057,0.16091,0.71226,0.71873,0.49675,0.49871,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70122,SRR19561942,SRX15614008,SRS13314713,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr13 1,Dr13 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:13 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 52 13 1 Brain,52 13 1 Brain,52 13 1 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6041 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,52-13-1-Brain-RNA_R1.fq.gz 52-13-1-Brain-RNA_R2.fq.gz,fastq fastq,6564342900.0,21881143.0,52 13 1 Brain RNA R1.fq.gz,0:150 1:150,A:1875036799;C:1388864833;G:1412506225;T:1887810961;N:124082,150,150,,,1875036799,1388864833,1412506225,1887810961,124082,SRX15614008,SRS13314713,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92113,0.9218,0.16856,0.16862,0.71147,0.71776,0.48601,0.50846,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70129,SRR19561949,SRX15614001,SRS13314712,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 3,Dr18 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 51 18 3 Brain,51 18 3 Brain,51 18 3 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6035 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,51-18-3-Brain-RNA_R1.fq.gz 51-18-3-Brain-RNA_R2.fq.gz,fastq fastq,6606239700.0,22020799.0,51 18 3 Brain RNA R1.fq.gz,0:150 1:150,A:1885996342;C:1397743068;G:1420407935;T:1901969274;N:123081,150,150,,,1885996342,1397743068,1420407935,1901969274,123081,SRX15614001,SRS13314712,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92037,0.92037,0.17349,0.17351,0.7134,0.71961,0.49757,0.5036,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70136,SRR19561956,SRX15613994,SRS13314711,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 2,Dr18 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 50 18 2 Brain,50 18 2 Brain,50 18 2 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6029 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,50-18-2-Brain-RNA_R1.fq.gz 50-18-2-Brain-RNA_R2.fq.gz,fastq fastq,6281424600.0,20938082.0,50 18 2 Brain RNA R1.fq.gz,0:150 1:150,A:1790409321;C:1331778838;G:1355326334;T:1803791514;N:118593,150,150,,,1790409321,1331778838,1355326334,1803791514,118593,SRX15613994,SRS13314711,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92329,0.92423,0.16356,0.16369,0.71788,0.72366,0.50986,0.51265,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70142,SRR19561962,SRX15613988,SRS13314710,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr18 1,Dr18 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:18 replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 49 18 1 Brain,49 18 1 Brain,49 18 1 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6023 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,49-18-1-Brain-RNA_R1.fq.gz 49-18-1-Brain-RNA_R2.fq.gz,fastq fastq,7316116800.0,24387056.0,49 18 1 Brain RNA R1.fq.gz,0:150 1:150,A:2029219672;C:1605053166;G:1629415583;T:2052291110;N:137269,150,150,,,2029219672,1605053166,1629415583,2052291110,137269,SRX15613988,SRS13314710,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92845,0.92831,0.15339,0.15343,0.70163,0.70818,0.50561,0.49113,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70149,SRR19561969,SRX15613981,SRS13314709,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 3,Dr27 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 48 27 3 Brain,48 27 3 Brain,48 27 3 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6017 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,48-27-3-Brain-RNA_R1.fq.gz 48-27-3-Brain-RNA_R2.fq.gz,fastq fastq,7425268800.0,24750896.0,48 27 3 Brain RNA R1.fq.gz,0:150 1:150,A:2180771736;C:1512927753;G:1541462587;T:2189964944;N:141780,150,150,,,2180771736,1512927753,1541462587,2189964944,141780,SRX15613981,SRS13314709,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.92505,0.92554,0.17225,0.17055,0.73162,0.73634,0.54078,0.54258,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
70155,SRR19561975,SRX15613975,SRS13314708,SRP378802,PRJNA846110,Danio rerio Raw sequence reads,PRJNA846110,Other,Temperature dependence of RNA editing in six tissues of the zebrafish Danio rerio,,,,Dr27 2,Dr27 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:adult|sex:female|tissue:multi tissue|aliquot:27 replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: adult female 47 27 2 Brain,47 27 2 Brain,47 27 2 Brain,All strand specific RNA seq libraries were constructed using VAHTS Stranded mRNA seq library Prep kit for Illumina v2  Vazyme Biotech Co.  Ltd  NR612 02  and subjected to 150bp paired end sequencing on a Novaseq 6011 illumina platform.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP378802,,,47-27-2-Brain-RNA_R1.fq.gz 47-27-2-Brain-RNA_R2.fq.gz,fastq fastq,8266981800.0,27556606.0,47 27 2 Brain RNA R1.fq.gz,0:150 1:150,A:2439238017;C:1674208335;G:1753393244;T:2400007685;N:134519,150,150,,,2439238017,1674208335,1753393244,2400007685,134519,SRX15613975,SRS13314708,SRA1432943,shanghai ocean university|College of Fisheries and Life Science,shanghai ocean university,2,0.93567,0.91255,0.15677,0.15133,0.73728,0.74059,0.58353,0.5211,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2022-06-07,Adult,Adult,Brain,Nervous System
75356,SRR24489425,SRX20274795,SRS17602489,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult Brain F5,F5 WT brain N R1 001,,strain:Tuebingen|isolate:WT Brain F5|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain WT,F5 WT brain N,F5 WT brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F5-WT-brain-N_R1_001.fastq.gz F5-WT-brain-N_R2_001.fastq.gz,fastq fastq,6841055400.0,22803518.0,F5 WT brain N R1 001.fastq.gz,0:150 1:150,A:1812654704;C:1604487806;G:1679235049;T:1744234054;N:443787,150,150,,,1812654704,1604487806,1679235049,1744234054,443787,SRX20274795,SRS17602489,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93773,0.93874,0.10994,0.10853,0.69426,0.69818,0.51982,0.52431,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75362,SRR24489431,SRX20274789,SRS17602483,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old KO Brain 6,Cygb1KO G 6 S32 R1 001,,strain:Tuebingen|isolate:Brain 6 Cygb1KO|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain Cygb1KO,Cygb1KO G 6S32,Cygb1KO G 6S32,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,Cygb1KO-G-6_S32_R1_001.fastq.gz Cygb1KO-G-6_S32_R2_001.fastq.gz,fastq fastq,9925695180.0,34149517.0,Cygb1KO G 6 S32 R1 001.fastq.gz,0:142.59 1:148.06,A:2929412339;C:1950048888;G:2154536328;T:2880617061;N:11080564,142,148,,,2929412339,1950048888,2154536328,2880617061,11080564,SRX20274789,SRS17602483,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.9273,0.92531,0.25488,0.2525,0.71794,0.71561,0.53653,0.53821,149,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75364,SRR24489433,SRX20274787,SRS17602478,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old KO Brain 4,Cygb1KO G 4 S31 R1 001,,strain:Tuebingen|isolate:Brain 4 Cygb1KO|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain Cygb1KO,Cygb1KO G 4S31,Cygb1KO G 4S31,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,Cygb1KO-G-4_S31_R1_001.fastq.gz Cygb1KO-G-4_S31_R2_001.fastq.gz,fastq fastq,9815347477.0,33708992.0,Cygb1KO G 4 S31 R1 001.fastq.gz,0:143.34 1:147.83,A:2847426769;C:1996151135;G:2157346007;T:2805302254;N:9121312,143,147,,,2847426769,1996151135,2157346007,2805302254,9121312,SRX20274787,SRS17602478,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93535,0.93362,0.22332,0.21868,0.70786,0.70579,0.51367,0.50733,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75366,SRR24489435,SRX20274785,SRS17602477,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old KO Brain 3,Cygb1KO G 3 S30 R1 001,,strain:Tuebingen|isolate:Brain 3 Cygb1KO|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain Cygb1KO,Cygb1KO G 3S30,Cygb1KO G 3S30,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,Cygb1KO-G-3_S30_R1_001.fastq.gz Cygb1KO-G-3_S30_R2_001.fastq.gz,fastq fastq,6375806624.0,22076571.0,Cygb1KO G 3 S30 R1 001.fastq.gz,0:140.65 1:148.15,A:1838824763;C:1269837958;G:1450334143;T:1807137695;N:9672065,140,148,,,1838824763,1269837958,1450334143,1807137695,9672065,SRX20274785,SRS17602477,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93667,0.93108,0.22667,0.22219,0.71131,0.70883,0.51796,0.50211,149,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75369,SRR24489438,SRX20274782,SRS17602473,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old KO Brain 2,Cygb1KO G 2 S29 R1 001,,strain:Tuebingen|isolate:Brain 2 Cygb1KO|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain Cygb1KO,Cygb1KO G 2S29,Cygb1KO G 2S29,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,Cygb1KO-G-2_S29_R1_001.fastq.gz Cygb1KO-G-2_S29_R2_001.fastq.gz,fastq fastq,9228083087.0,31353095.0,Cygb1KO G 2 S29 R1 001.fastq.gz,0:146.81 1:147.51,A:2685482962;C:1925153227;G:1961258559;T:2654447279;N:1741060,146,147,,,2685482962,1925153227,1961258559,2654447279,1741060,SRX20274782,SRS17602473,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.94076,0.94161,0.20564,0.20278,0.70498,0.70157,0.51187,0.51437,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75371,SRR24489440,SRX20274780,SRS17602476,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old Brain 4,4 brainWTm R1 001,,strain:Tuebingen|isolate:Old Brain 4|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain WT,4 brainWTm,4 brainWTm,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,4-brainWTm_R1_001.fastq.gz 4-brainWTm_R2_001.fastq.gz,fastq fastq,5391512414.0,18695220.0,4 brainWTm R1 001.fastq.gz,0:143.36 1:145.03,A:1526986732;C:1144838870;G:1197115002;T:1511509189;N:11062621,143,145,,,1526986732,1144838870,1197115002,1511509189,11062621,SRX20274780,SRS17602476,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93479,0.93458,0.18008,0.17489,0.70652,0.70772,0.52976,0.52891,150,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75373,SRR24489442,SRX20274778,SRS17602472,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old Brain 3,3 brainWTm R1 001,,strain:Tuebingen|isolate:Old Brain 3|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain WT,3 brainWTm,3 brainWTm,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,3-brainWTm_R1_001.fastq.gz 3-brainWTm_R2_001.fastq.gz,fastq fastq,7193574753.0,25032649.0,3 brainWTm R1 001.fastq.gz,0:143.01 1:144.35,A:2045307156;C:1525864162;G:1582858563;T:2027473626;N:12071246,143,144,,,2045307156,1525864162,1582858563,2027473626,12071246,SRX20274778,SRS17602472,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93262,0.93305,0.18864,0.18297,0.70522,0.70755,0.52309,0.50982,149,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75375,SRR24489444,SRX20274776,SRS17602470,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old Brain 2,2 brainWTm R1 001,,strain:Tuebingen|isolate:Old Brain 2|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain WT,2 brainWTm,2 brainWTm,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,2-brainWTm_R1_001.fastq.gz 2-brainWTm_R2_001.fastq.gz,fastq fastq,6187362464.0,21465519.0,2 brainWTm R1 001.fastq.gz,0:143.41 1:144.83,A:1748094759;C:1321274648;G:1378525698;T:1728446529;N:11020830,143,144,,,1748094759,1321274648,1378525698,1728446529,11020830,SRX20274776,SRS17602470,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93634,0.93569,0.19002,0.18498,0.70583,0.70912,0.49674,0.50861,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75377,SRR24489446,SRX20274774,SRS17602469,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Old Brain 1,1 brainWTm R1 001,,strain:Tuebingen|isolate:Old Brain 1|age:24 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 24mpf Brain WT,1 brainWTm,1 brainWTm,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP436765,,,1-brainWTm_R1_001.fastq.gz 1-brainWTm_R2_001.fastq.gz,fastq fastq,6726100792.0,23362002.0,1 brainWTm R1 001.fastq.gz,0:143.27 1:144.64,A:1908300690;C:1425875188;G:1484609343;T:1896451119;N:10864452,143,144,,,1908300690,1425875188,1484609343,1896451119,10864452,SRX20274774,SRS17602469,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93315,0.93389,0.18871,0.18572,0.70763,0.70867,0.51666,0.51966,148,148,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75380,SRR24489449,SRX20274771,SRS17602465,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult KO brain F8,F8 KO brain N R1 001,,strain:Tuebingen|isolate:KO brain F8|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain Cygb1KO,F8 KO brain N,F8 KO brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F8-KO-brain-N_R1_001.fastq.gz F8-KO-brain-N_R2_001.fastq.gz,fastq fastq,6510417300.0,21701391.0,F8 KO brain N R1 001.fastq.gz,0:150 1:150,A:1728085662;C:1527176393;G:1597814846;T:1656898844;N:441555,150,150,,,1728085662,1527176393,1597814846,1656898844,441555,SRX20274771,SRS17602465,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93609,0.93632,0.11539,0.11374,0.69321,0.69818,0.50708,0.51603,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75382,SRR24489451,SRX20274769,SRS17602474,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult KO brain F4,F4 KO brain N R1 001,,strain:Tuebingen|isolate:KO brain F4|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain Cygb1KO,F4 KO brain N,F4 KO brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F4-KO-brain-N_R1_001.fastq.gz F4-KO-brain-N_R2_001.fastq.gz,fastq fastq,6297273000.0,20990910.0,F4 KO brain N R1 001.fastq.gz,0:150 1:150,A:1650938116;C:1498344277;G:1568940240;T:1578646981;N:403386,150,150,,,1650938116,1498344277,1568940240,1578646981,403386,SRX20274769,SRS17602474,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.95268,0.95128,0.10086,0.09863,0.70396,0.70873,0.53685,0.54149,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75384,SRR24489453,SRX20274767,SRS17602462,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult KO brain F1,F1 KO brain N R1 001,,strain:Tuebingen|isolate:KO brain F1|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:cygb1 knockout|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain Cygb1KO,F1 KO brain N,F1 KO brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F1-KO-brain-N_R1_001.fastq.gz F1-KO-brain-N_R2_001.fastq.gz,fastq fastq,6723614100.0,22412047.0,F1 KO brain N R1 001.fastq.gz,0:150 1:150,A:1794142191;C:1565642043;G:1634809983;T:1728587385;N:432498,150,150,,,1794142191,1565642043,1634809983,1728587385,432498,SRX20274767,SRS17602462,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.94665,0.94595,0.1223,0.12114,0.68799,0.69315,0.51146,0.49845,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75386,SRR24489455,SRX20274765,SRS17602459,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult Brain F7,F7 WT brain N R1 001,,strain:Tuebingen|isolate:WT Brain F7|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain WT,F7 WT brain N,F7 WT brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F7-WT-brain-N_R1_001.fastq.gz F7-WT-brain-N_R2_001.fastq.gz,fastq fastq,6576419700.0,21921399.0,F7 WT brain N R1 001.fastq.gz,0:150 1:150,A:1752976243;C:1536177292;G:1602467003;T:1684351538;N:447624,150,150,,,1752976243,1536177292,1602467003,1684351538,447624,SRX20274765,SRS17602459,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.93786,0.93818,0.12172,0.12012,0.68722,0.69158,0.51031,0.50836,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System
75388,SRR24489457,SRX20274763,SRS17602458,SRP436765,PRJNA970658,Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio,PRJNA970658,Other,Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification  NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies  including neoplasia of gonads  and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.,,,,Adult Brain F6,F6 WT brain N R1 001,,strain:Tuebingen|isolate:WT Brain F6|age:12 mpf|dev stage:adult|sex:male|tissue:brain|genotype:wildtype|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq Zebrafish 12mpf Brain WT,F6 WT brain N,F6 WT brain N,Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen  according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP436765,,,F6-WT-brain-N_R1_001.fastq.gz F6-WT-brain-N_R2_001.fastq.gz,fastq fastq,5529906000.0,18433020.0,F6 WT brain N R1 001.fastq.gz,0:150 1:150,A:1484087685;C:1276380609;G:1344707858;T:1424369191;N:360657,150,150,,,1484087685,1276380609,1344707858,1424369191,360657,SRX20274763,SRS17602458,SRA1634682,University of Hamburg|Institute of Animal Cell and Systems Biology (IZS),University of Hamburg,2,0.92807,0.92821,0.12062,0.11965,0.69126,0.69702,0.50832,0.51172,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2023-05-10,Adult,Adult,Brain,Nervous System