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
0,DRR314108,DRX303511,DRS233566,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample3,SAMD00399013,,sample name:rna rw337 48hpf WT rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399013,DRX303511,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399013,,,,23076492885.0,76679376.0,DRR314108,0:150.51 1:150.44,A:6146969533;C:5373690527;G:5458576301;T:6095818756;N:1437768,150,150,,,6146969533,5373690527,5458576301,6095818756,1437768,DRX303511,DRS233566,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94223,0.94614,0.10721,0.10288,0.68745,0.68621,0.4728,0.47157,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
1,DRR314107,DRX303510,DRS233565,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample2,SAMD00399012,,sample name:rna rw337 48hpf WT rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399012,DRX303510,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399012,,,,26091623771.0,86694066.0,DRR314107,0:150.51 1:150.45,A:6955374552;C:6050013285;G:6169385096;T:6915281392;N:1569446,150,150,,,6955374552,6050013285,6169385096,6915281392,1569446,DRX303510,DRS233565,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94028,0.94277,0.11038,0.10462,0.68288,0.68134,0.46992,0.47227,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
2,DRR314106,DRX303509,DRS233564,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample1,SAMD00399011,,sample name:rna rw337 48hpf WT rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399011,DRX303509,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399011,,,,23833525756.0,79191795.0,DRR314106,0:150.51 1:150.44,A:6324521565;C:5556755459;G:5694025045;T:6256748423;N:1475264,150,150,,,6324521565,5556755459,5694025045,6256748423,1475264,DRX303509,DRS233564,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94723,0.94975,0.09521,0.09114,0.6776,0.67819,0.46045,0.46153,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
3,DRR314105,DRX303508,DRS233563,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample3,SAMD00399010,,sample name:rna rw337 48hpf Mutant rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399010,DRX303508,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399010,,,,27688386114.0,92009317.0,DRR314105,0:150.49 1:150.44,A:7681451080;C:6071566134;G:6242782106;T:7690830655;N:1756139,150,150,,,7681451080,6071566134,6242782106,7690830655,1756139,DRX303508,DRS233563,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.91038,0.91556,0.17971,0.16967,0.67718,0.67716,0.47042,0.46425,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
4,DRR314104,DRX303507,DRS233562,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample2,SAMD00399009,,sample name:rna rw337 48hpf Mutant rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399009,DRX303507,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399009,,,,22970994572.0,76322352.0,DRR314104,0:150.52 1:150.46,A:6142535654;C:5310453740;G:5430124468;T:6086516676;N:1364034,150,150,,,6142535654,5310453740,5430124468,6086516676,1364034,DRX303507,DRS233562,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.93707,0.94063,0.12175,0.11613,0.67825,0.67649,0.46485,0.46905,147,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
5,DRR314103,DRX303506,DRS233561,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp  the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample1,SAMD00399008,,sample name:rna rw337 48hpf Mutant rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399008,DRX303506,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399008,,,,23637901630.0,78541449.0,DRR314103,0:150.51 1:150.45,A:6359178134;C:5420730443;G:5530700546;T:6325864263;N:1428244,150,150,,,6359178134,5420730443,5530700546,6325864263,1428244,DRX303506,DRS233561,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.9308,0.93545,0.13172,0.12462,0.68219,0.6814,0.46842,0.46984,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
6,DRR315802,DRX305194,DRS231989,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample4,SAMD00400823,,sample name:rw147 2.5dpf wildtype  rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,DRX305194,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,,,,10262353995.0,34151547.0,DRR315802,0:150.27 1:150.22,A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550,150,150,,,2735078560,2386126821,2433638250,2707202814,307550,DRX305194,DRS231989,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95231,0.95295,0.09229,0.08773,0.71819,0.72107,0.46746,0.46617,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
7,DRR315801,DRX305193,DRS231988,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample3,SAMD00400822,,sample name:rw147 2.5dpf wildtype  rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,DRX305193,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,,,,11516368634.0,38355888.0,DRR315801,0:150.15 1:150.10,A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954,150,150,,,3080341643,2678048339,2713051368,3044449330,477954,DRX305193,DRS231988,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95353,0.95634,0.08909,0.08533,0.71374,0.71252,0.45986,0.46059,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
8,DRR315800,DRX305192,DRS231987,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample2,SAMD00400821,,sample name:rw147 2.5dpf wildtype  rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,DRX305192,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,,,,8814057148.0,29367513.0,DRR315800,0:150.09 1:150.04,A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957,150,150,,,2350403211,2054073465,2083044327,2326181188,354957,DRX305192,DRS231987,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95287,0.95643,0.0891,0.08586,0.70309,0.70252,0.46384,0.46281,151,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
9,DRR315799,DRX305191,DRS231986,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample1,SAMD00400820,,sample name:rw147 2.5dpf wildtype  rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,DRX305191,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,,,,10491955578.0,34900682.0,DRR315799,0:150.34 1:150.28,A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831,150,150,,,2796521111,2446218287,2483414564,2765477785,323831,DRX305191,DRS231986,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9539,0.95646,0.08185,0.07808,0.70025,0.70013,0.44713,0.44987,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
10,DRR315798,DRX305190,DRS231985,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample4,SAMD00400819,,sample name:rw147 2.5dpf Mutant  rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,DRX305190,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,,,,9197802250.0,30604326.0,DRR315798,0:150.30 1:150.24,A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028,150,150,,,2468967963,2130949980,2158692262,2438931017,261028,DRX305190,DRS231985,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95159,0.95439,0.10146,0.09758,0.71995,0.71983,0.46519,0.46797,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
11,DRR315797,DRX305189,DRS231984,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample3,SAMD00400818,,sample name:rw147 2.5dpf Mutant  rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,DRX305189,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,,,,10498982078.0,34931731.0,DRR315797,0:150.31 1:150.25,A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945,150,150,,,2804535103,2445295179,2478768789,2770066062,316945,DRX305189,DRS231984,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95448,0.95652,0.0939,0.0887,0.71796,0.71847,0.46335,0.46615,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
12,DRR315796,DRX305188,DRS231983,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample2,SAMD00400817,,sample name:rw147 2.5dpf Mutant  rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,DRX305188,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,,,,9850145990.0,32782079.0,DRR315796,0:150.26 1:150.21,A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024,150,150,,,2636205537,2286508705,2319481100,2607600624,350024,DRX305188,DRS231983,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95193,0.95472,0.09722,0.09375,0.7138,0.71299,0.45542,0.45994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
13,DRR315795,DRX305187,DRS231982,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample1,SAMD00400816,,sample name:rw147 2.5dpf Mutant  rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,DRX305187,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,,,,9542039835.0,31780260.0,DRR315795,0:150.15 1:150.10,A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225,150,150,,,2543384204,2224374632,2258183435,2515655339,442225,DRX305187,DRS231982,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9528,0.95591,0.08656,0.0828,0.70352,0.70331,0.45316,0.44914,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
10383,ERR8517249,ERX8083723,ERS10517669,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 003,SAMEA12918519,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918519|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 003|common name:zebrafish|sample name:hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 003,webin reads hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_003_R1.fastq.gz hnRNPK_003_R2.fastq.gz,fastq fastq,2931486932.0,19421721.0,webin reads hnRNPK 003,0:75.51 1:75.43,A:759548162;C:700272829;G:700149526;T:770783019;N:733396,75,75,,,759548162,700272829,700149526,770783019,733396,ERX8083723,ERS10517669,ERA8937191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.9621,0.96378,0.06994,0.06876,0.68757,0.68998,0.46746,0.47041,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10384,ERR8517226,ERX8083700,ERS10517665,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier control,hnRNPK 001,SAMEA12918515,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918515|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:hnRNPK 001|common name:zebrafish|sample name:hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: hnRNPK 001,webin reads hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,hnRNPK_001_R1.fastq.gz hnRNPK_001_R2.fastq.gz,fastq fastq,2728299749.0,18074835.0,webin reads hnRNPK 001,0:75.51 1:75.43,A:710869412;C:649804308;G:644363972;T:722599378;N:662679,75,75,,,710869412,649804308,644363972,722599378,662679,ERX8083700,ERS10517665,ERA8936710,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96092,0.96336,0.07296,0.07144,0.68862,0.69209,0.47036,0.47104,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10385,ERR8517194,ERX8083668,ERS10517668,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 003,SAMEA12918518,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918518|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 003|common name:zebrafish|sample name:GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 003,webin reads GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_003_R1.fastq.gz GFP_003_R2.fastq.gz,fastq fastq,2845571506.0,18850866.0,webin reads GFP 003,0:75.52 1:75.43,A:737412560;C:678774596;G:684567775;T:744108157;N:708418,75,75,,,737412560,678774596,684567775,744108157,708418,ERX8083668,ERS10517668,ERA8936242,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96279,0.96355,0.06774,0.06607,0.68864,0.69183,0.469,0.46906,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10386,ERR8517159,ERX8083633,ERS10517664,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,RNA control,GFP 001,SAMEA12918514,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918514|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:GFP 001|common name:zebrafish|sample name:GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: GFP 001,webin reads GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,GFP_001_R1.fastq.gz GFP_001_R2.fastq.gz,fastq fastq,2873485447.0,19035162.0,webin reads GFP 001,0:75.52 1:75.44,A:746120172;C:687054955;G:682142981;T:757435799;N:731540,75,75,,,746120172,687054955,682142981,757435799,731540,ERX8083633,ERS10517664,ERA8935703,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96176,0.96461,0.07014,0.06932,0.68672,0.68913,0.47006,0.46794,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10387,ERR8517115,ERX8083589,ERS10517671,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 003,SAMEA12918521,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918521|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 003|common name:zebrafish|sample name:91S hnRNPK 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 003,webin reads 91S hnRNPK 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_003_R1.fastq.gz 91S_hnRNPK_003_R2.fastq.gz,fastq fastq,2853403405.0,18902398.0,webin reads 91S hnRNPK 003,0:75.52 1:75.44,A:739541111;C:681340573;G:681790014;T:750013318;N:718389,75,75,,,739541111,681340573,681790014,750013318,718389,ERX8083589,ERS10517671,ERA8935191,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96234,0.96429,0.0679,0.06627,0.68984,0.69126,0.46434,0.47087,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10388,ERR8517082,ERX8083556,ERS10517667,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Modifier rescue,91S hnRNPK 001,SAMEA12918517,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918517|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S hnRNPK 001|common name:zebrafish|sample name:91S hnRNPK 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S hnRNPK 001,webin reads 91S hnRNPK 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S hnRNPK 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_hnRNPK_001_R1.fastq.gz 91S_hnRNPK_001_R2.fastq.gz,fastq fastq,2795603091.0,18519699.0,webin reads 91S hnRNPK 001,0:75.52 1:75.43,A:722724564;C:672552332;G:664566386;T:735058575;N:701234,75,75,,,722724564,672552332,664566386,735058575,701234,ERX8083556,ERS10517667,ERA8934579,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96307,0.96547,0.06551,0.06458,0.68714,0.68856,0.46817,0.46555,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10389,ERR8517039,ERX8083513,ERS10517670,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 003,SAMEA12918520,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918520|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 003|common name:zebrafish|sample name:91S GFP 003,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 003,webin reads 91S GFP 003,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 003,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_003_R1.fastq.gz 91S_GFP_003_R2.fastq.gz,fastq fastq,2946600193.0,19521826.0,webin reads 91S GFP 003,0:75.51 1:75.43,A:763284580;C:704439363;G:702989767;T:775149110;N:737373,75,75,,,763284580,704439363,702989767,775149110,737373,ERX8083513,ERS10517670,ERA8933888,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96151,0.96295,0.06621,0.06481,0.68807,0.69092,0.46928,0.46982,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
10390,ERR8516998,ERX8083472,ERS10517666,ERP135370,PRJEB50765,HNRNPK alleviates RNA toxicity by counteracting DNA damage in C9orf72 ALS,69e2093b-755e-4be3-88b8-5b4a761258fe,Other,A 'GGGGCC' repeat expansion in the first intron of the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis ALS and frontotemporal dementia FTD. The exact mechanism resulting in these neurodegenerative diseases remains elusive  but RNA toxicity has been implicated as a gain of function mechanism. Our aim was to use a zebrafish model for C9orf72 RNA toxicity to identify modifiers of the ALS linked phenotype. We discovered that the RNA binding protein heterogeneous nuclear ribonucleoprotein K HNRNPK can reverse the toxicity of both sense and antisense repeat RNA  which is dependent on its subcellular localization and on RNA recognition  and not on C9 repeat RNA binding. We observed HNRNPK cytoplasmic mislocalization in C9orf72 ALS patient fibroblasts  induced pluripotent stem cell iPSC derived motor neurons and postmortem central cortex  suggesting a disrupted HNRNPK function in C9orf72 ALS. In C9 ALS/FTD patient tissue  we discovered an increased nuclear translocation  but reduced expression of Ribonucleotide Reductase Regulatory Subunit M2 RRM2  a downstream target of HNRNPK involved in DNA damage response. Finally  we show that increasing the expression of HNRNPK or RRM2 was sufficient to mitigate DNA damage in our C9 RNA toxicity zebrafish model. Overall  our study strengthens the relevance of RNA toxicity as a pathogenic mechanism in C9 ALS and demonstrates its link with aberrant DNA damage response  opening novel therapeutic strategies for C9 ALS/FTD.,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,PUBMED:29302778;PUBMED:35895140,Toxic condition,91S GFP 001,SAMEA12918516,vib-ku leuven,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22|External Id:SAMEA12918516|INSDC center alias:VIB KU Leuven|INSDC center name:vib ku leuven|INSDC first public:2022 08 22T12:15:26Z|INSDC last update:2022 08 22T12:15:26Z|INSDC status:public|Submitter Id:91S GFP 001|common name:zebrafish|sample name:91S GFP 001,,,,,,,,,NextSeq 500 paired end sequencing; Raw reads: 91S GFP 001,webin reads 91S GFP 001,,unspecified,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP135370,Raw reads: 91S GFP 001,ENA FIRST PUBLIC:2022 08 22|ENA LAST UPDATE:2022 08 22,91S_GFP_001_R1.fastq.gz 91S_GFP_001_R2.fastq.gz,fastq fastq,2821113913.0,18686946.0,webin reads 91S GFP 001,0:75.52 1:75.44,A:726676187;C:676899384;G:676400816;T:740427303;N:710223,75,75,,,726676187,676899384,676400816,740427303,710223,ERX8083472,ERS10517666,ERA8933211,vib-ku leuven|European Nucleotide Archive,vib-ku leuven,2,0.96147,0.96465,0.07106,0.06991,0.68822,0.69556,0.47261,0.47451,75,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Belgium,2022-08-22,Undetermined,Undetermined,Undetermined,Undetermined
34286,SRR31640761,SRX27004206,SRS23468965,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 3,BXP 3,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-3_1.fq.gz BXP-3_2.fq.gz,fastq fastq,6830689200.0,22768964.0,BXP 3 1.fq.gz,0:150 1:150,A:1937590708;C:1484093984;G:1501320204;T:1907663118;N:21186,150,150,,,1937590708,1484093984,1501320204,1907663118,21186,SRX27004206,SRS23468965,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34287,SRR31640762,SRX27004205,SRS23468964,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 2,BXP 2,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-2_1.fq.gz BXP-2_2.fq.gz,fastq fastq,6779695800.0,22598986.0,BXP 2 1.fq.gz,0:150 1:150,A:1940362424;C:1457342925;G:1474251255;T:1907718219;N:20977,150,150,,,1940362424,1457342925,1474251255,1907718219,20977,SRX27004205,SRS23468964,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34288,SRR31640763,SRX27004204,SRS23468967,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 1,BXP 1,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-1_1.fq.gz BXP-1_2.fq.gz,fastq fastq,6565466100.0,21884887.0,BXP 1 1.fq.gz,0:150 1:150,A:1875205670;C:1413467668;G:1430939925;T:1845830468;N:22369,150,150,,,1875205670,1413467668,1430939925,1845830468,22369,SRX27004204,SRS23468967,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34289,SRR31640764,SRX27004203,SRS23468966,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 3,Control 3,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-3_1.fq.gz Control-3_2.fq.gz,fastq fastq,6430890900.0,21436303.0,Control 3 1.fq.gz,0:150 1:150,A:1836469770;C:1387135442;G:1409220900;T:1798042594;N:22194,150,150,,,1836469770,1387135442,1409220900,1798042594,22194,SRX27004203,SRS23468966,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34292,SRR31640767,SRX27004200,SRS23468963,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 2,Control 2,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-2_1.fq.gz Control-2_2.fq.gz,fastq fastq,6980411100.0,23268037.0,Control 2 1.fq.gz,0:150 1:150,A:1967066686;C:1535551736;G:1553468906;T:1924299656;N:24116,150,150,,,1967066686,1535551736,1553468906,1924299656,24116,SRX27004200,SRS23468963,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34293,SRR31640768,SRX27004199,SRS23468962,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 1,Control 1,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-1_1.fq.gz Control-1_2.fq.gz,fastq fastq,6893069100.0,22976897.0,Control 1 1.fq.gz,0:150 1:150,A:1990628725;C:1465163855;G:1482329167;T:1954923719;N:23634,150,150,,,1990628725,1465163855,1482329167,1954923719,23634,SRX27004199,SRS23468962,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-09,Undetermined,Larval,Undetermined,Undetermined
36032,SRR33405556,SRX28646822,SRS24917431,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut2 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut2 d2,mut2 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_mut-2_S6_R1_001.fastq.gz y680_mut-2_S6_R2_001.fastq.gz,fastq fastq,13048391588.0,65176490.0,y680 mut 2 S6 R1 001.fastq.gz,0:100.12 1:100.08,A:3382606790;C:3166963239;G:3249911967;T:3247119183;N:1790409,100,100,,,3382606790,3166963239,3249911967,3247119183,1790409,SRX28646822,SRS24917431,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36033,SRR33405557,SRX28646821,SRS24917430,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut1 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut1 d2,mut1 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_mut-1_S5_R1_001.fastq.gz y680_mut-1_S5_R2_001.fastq.gz,fastq fastq,11244387522.0,56145229.0,y680 mut 1 S5 R1 001.fastq.gz,0:100.15 1:100.12,A:2893088657;C:2737659501;G:2830491662;T:2781546759;N:1600943,100,100,,,2893088657,2737659501,2830491662,2781546759,1600943,SRX28646821,SRS24917430,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36034,SRR33405558,SRX28646820,SRS24917429,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het4 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het4 d2,het4 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_het-4_S4_R1_001.fastq.gz y680_het-4_S4_R2_001.fastq.gz,fastq fastq,7488095202.0,37372687.0,y680 het 4 S4 R1 001.fastq.gz,0:100.20 1:100.16,A:1931359037;C:1813371312;G:1880760315;T:1861860377;N:744161,100,100,,,1931359037,1813371312,1880760315,1861860377,744161,SRX28646820,SRS24917429,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36035,SRR33405559,SRX28646819,SRS24917428,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het3 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het3 d2,het3 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_het-3_S3_R1_001.fastq.gz y680_het-3_S3_R2_001.fastq.gz,fastq fastq,13441009956.0,67072919.0,y680 het 3 S3 R1 001.fastq.gz,0:100.22 1:100.18,A:3484306615;C:3249847841;G:3351167195;T:3353988961;N:1699344,100,100,,,3484306615,3249847841,3351167195,3353988961,1699344,SRX28646819,SRS24917428,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36036,SRR33405560,SRX28646818,SRS24917427,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het2 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het2 d2,het2 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_het-2_S2_R1_001.fastq.gz y680_het-2_S2_R2_001.fastq.gz,fastq fastq,10048330828.0,50202819.0,y680 het 2 S2 R1 001.fastq.gz,0:100.10 1:100.05,A:2557623639;C:2473642678;G:2526118363;T:2490175343;N:770805,100,100,,,2557623639,2473642678,2526118363,2490175343,770805,SRX28646818,SRS24917427,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36037,SRR33405561,SRX28646817,SRS24917426,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het1 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het1 d2,het1 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_het-1_S1_R1_001.fastq.gz y680_het-1_S1_R2_001.fastq.gz,fastq fastq,21241485328.0,106063264.0,y680 het 1 S1 R1 001.fastq.gz,0:100.16 1:100.11,A:5428876256;C:5216202525;G:5316134708;T:5278092708;N:2179131,100,100,,,5428876256,5216202525,5316134708,5278092708,2179131,SRX28646817,SRS24917426,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36038,SRR33405562,SRX28646816,SRS24917425,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt4 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt4 d2,wt4 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680-WT-4_S56_R1_001.fastq.gz y680-WT-4_S56_R2_001.fastq.gz,fastq fastq,2871774704.0,14403351.0,y680 WT 4 S56 R1 001.fastq.gz,0:99.62 1:99.76,A:738963438;C:693060627;G:725455885;T:712804013;N:1490741,99,99,,,738963438,693060627,725455885,712804013,1490741,SRX28646816,SRS24917425,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36039,SRR33405563,SRX28646815,SRS24917424,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut3 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 6 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut3 d6,mut3 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_mut_3_S6_R1_001.fastq.gz cacna1c_mut_3_S6_R2_001.fastq.gz,fastq fastq,10821244875.0,54211675.0,cacna1c mut 3 S6 R1 001.fastq.gz,0:99.80 1:99.81,A:2844936671;C:2560986718;G:2541107233;T:2872530750;N:1683503,99,99,,,2844936671,2560986718,2541107233,2872530750,1683503,SRX28646815,SRS24917424,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36040,SRR33405564,SRX28646814,SRS24917423,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt3 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt3 d2,wt3 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_WT-3_S11_R1_001.fastq.gz y680_WT-3_S11_R2_001.fastq.gz,fastq fastq,4644100900.0,23208636.0,y680 WT 3 S11 R1 001.fastq.gz,0:100.02 1:100.08,A:1208863635;C:1115875593;G:1183409664;T:1134173818;N:1778190,100,100,,,1208863635,1115875593,1183409664,1134173818,1778190,SRX28646814,SRS24917423,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36041,SRR33405565,SRX28646813,SRS24917422,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut2 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 6 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut2 d6,mut2 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_mut_2_S5_R1_001.fastq.gz cacna1c_mut_2_S5_R2_001.fastq.gz,fastq fastq,10304033250.0,51767250.0,cacna1c mut 2 S5 R1 001.fastq.gz,0:99.52 1:99.53,A:2716459149;C:2428996746;G:2414245924;T:2742596672;N:1734759,99,99,,,2716459149,2428996746,2414245924,2742596672,1734759,SRX28646813,SRS24917422,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36042,SRR33405566,SRX28646812,SRS24917421,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut1 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 6 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut1 d6,mut1 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_mut_1_S4_R1_001.fastq.gz cacna1c_mut_1_S4_R2_001.fastq.gz,fastq fastq,10634669340.0,53207173.0,cacna1c mut 1 S4 R1 001.fastq.gz,0:99.94 1:99.94,A:2785021240;C:2526035959;G:2514333775;T:2807802849;N:1475517,99,99,,,2785021240,2526035959,2514333775,2807802849,1475517,SRX28646812,SRS24917421,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36043,SRR33405567,SRX28646811,SRS24917420,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het3 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 6 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het3 d6,het3 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_het_3_S3_R1_001.fastq.gz cacna1c_het_3_S3_R2_001.fastq.gz,fastq fastq,11351674291.0,56743676.0,cacna1c het 3 S3 R1 001.fastq.gz,0:100.02 1:100.03,A:2962013830;C:2707561654;G:2677851652;T:3002283466;N:1963689,100,100,,,2962013830,2707561654,2677851652,3002283466,1963689,SRX28646811,SRS24917420,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36044,SRR33405568,SRX28646810,SRS24917419,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het2 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 6 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het2 d6,het2 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_het_2_S2_R1_001.fastq.gz cacna1c_het_2_S2_R2_001.fastq.gz,fastq fastq,13026455522.0,65220604.0,cacna1c het 2 S2 R1 001.fastq.gz,0:99.83 1:99.90,A:3393911986;C:3106755468;G:3103867426;T:3417706604;N:4214038,99,99,,,3393911986,3106755468,3103867426,3417706604,4214038,SRX28646810,SRS24917419,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36045,SRR33405569,SRX28646809,SRS24917418,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,het1 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 6 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,het1 d6,het1 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_het_1_S1_R1_001.fastq.gz cacna1c_het_1_S1_R2_001.fastq.gz,fastq fastq,11684421424.0,58481596.0,cacna1c het 1 S1 R1 001.fastq.gz,0:99.90 1:99.89,A:3045294891;C:2793948277;G:2758390754;T:3085023344;N:1764158,99,99,,,3045294891,2793948277,2758390754,3085023344,1764158,SRX28646809,SRS24917418,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36046,SRR33405570,SRX28646808,SRS24917417,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt3 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 6 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt3 d6,wt3 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_WT_3_S9_R1_001.fastq.gz cacna1c_WT_3_S9_R2_001.fastq.gz,fastq fastq,17136980074.0,85761827.0,cacna1c WT 3 S9 R1 001.fastq.gz,0:99.89 1:99.93,A:4469122154;C:4093545051;G:4066811838;T:4502828568;N:4672463,99,99,,,4469122154,4093545051,4066811838,4502828568,4672463,SRX28646808,SRS24917417,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36047,SRR33405571,SRX28646807,SRS24917416,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt2 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 6 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt2 d6,wt2 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_WT_2_S8_R1_001.fastq.gz cacna1c_WT_2_S8_R2_001.fastq.gz,fastq fastq,11168393394.0,55950613.0,cacna1c WT 2 S8 R1 001.fastq.gz,0:99.79 1:99.82,A:2909422847;C:2666592302;G:2648992956;T:2940684477;N:2700812,99,99,,,2909422847,2666592302,2648992956,2940684477,2700812,SRX28646807,SRS24917416,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36048,SRR33405572,SRX28646806,SRS24917415,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt1 d6,,strain:ABC|age:6 dpf|collection date:2023 11|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 6 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt1 d6,wt1 d6,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,cacna1c_WT_1_S7_R1_001.fastq.gz cacna1c_WT_1_S7_R2_001.fastq.gz,fastq fastq,9293528237.0,46558667.0,cacna1c WT 1 S7 R1 001.fastq.gz,0:99.79 1:99.82,A:2430900099;C:2210330384;G:2204776815;T:2445836511;N:1684428,99,99,,,2430900099,2210330384,2204776815,2445836511,1684428,SRX28646806,SRS24917415,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Larval,Larval,Undetermined,Undetermined
36049,SRR33405573,SRX28646805,SRS24917414,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut4 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut4 d2,mut4 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_mut-4_S8_R1_001.fastq.gz y680_mut-4_S8_R2_001.fastq.gz,fastq fastq,6364246187.0,31799210.0,y680 mut 4 S8 R1 001.fastq.gz,0:100.05 1:100.09,A:1644746630;C:1536469430;G:1617907325;T:1562993280;N:2129522,100,100,,,1644746630,1536469430,1617907325,1562993280,2129522,SRX28646805,SRS24917414,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36050,SRR33405574,SRX28646804,SRS24917413,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,mut3 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,mut3 d2,mut3 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_mut-3_S7_R1_001.fastq.gz y680_mut-3_S7_R2_001.fastq.gz,fastq fastq,12769594212.0,63754551.0,y680 mut 3 S7 R1 001.fastq.gz,0:100.17 1:100.12,A:3270488183;C:3128646350;G:3212521095;T:3156861188;N:1077396,100,100,,,3270488183,3128646350,3212521095,3156861188,1077396,SRX28646804,SRS24917413,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36051,SRR33405575,SRX28646803,SRS24917412,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt2 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt2 d2,wt2 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680-WT-2_S40_R1_001.fastq.gz y680-WT-2_S40_R2_001.fastq.gz,fastq fastq,7228768016.0,36426014.0,y680 WT 2 S40 R1 001.fastq.gz,0:99.18 1:99.27,A:1808349692;C:1804255213;G:1817770107;T:1795596464;N:2796540,99,99,,,1808349692,1804255213,1817770107,1795596464,2796540,SRX28646803,SRS24917412,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36052,SRR33405576,SRX28646802,SRS24917411,SRP582714,PRJNA1257950,Zebrafish Timothy syndrome knock in model,PRJNA1257950,Other,Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.,,,,,wt1 d2,,strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland  Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish TS2 mutant,wt1 d2,wt1 d2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP582714,,,y680_WT-1_S9_R1_001.fastq.gz y680_WT-1_S9_R2_001.fastq.gz,fastq fastq,6639999850.0,33169283.0,y680 WT 1 S9 R1 001.fastq.gz,0:100.08 1:100.10,A:1706100512;C:1614640504;G:1665440844;T:1651930739;N:1887251,100,100,,,1706100512,1614640504,1665440844,1651930739,1887251,SRX28646802,SRS24917411,SRA2122396,NICHD|DDB,NICHD,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2025-05-01,Hatching,Embryo,Undetermined,Embryo Imprecise
36214,SRR33581822,SRX28811683,SRS25048556,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L3,,strain:Not collected|isolate:Rg1 L3|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:9|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L3,Rg1 L3,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D4_1.fq.gz D4_2.fq.gz,fastq fastq,6696495000.0,22321650.0,D4 1.fq.gz,0:150 1:150,A:1846856660;C:1513002602;G:1504866522;T:1831769216;N:0,150,150,,,1846856660,1513002602,1504866522,1831769216,0,SRX28811683,SRS25048556,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36215,SRR33581823,SRX28811682,SRS25048555,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L7,,strain:Not collected|isolate:Rg1 L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:8|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L7,Rg1 L7,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D2_1.fq.gz D2_2.fq.gz,fastq fastq,6666041700.0,22220139.0,D2 1.fq.gz,0:150 1:150,A:1845276816;C:1500512488;G:1492917547;T:1827334849;N:0,150,150,,,1845276816,1500512488,1492917547,1827334849,0,SRX28811682,SRS25048555,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36216,SRR33581824,SRX28811681,SRS25048554,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Rg1 L5,,strain:Not collected|isolate:Rg1 L5|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:7|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Treatment,Rg1 L5,Rg1 L5,Treatment,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,D1_1.fq.gz D1_2.fq.gz,fastq fastq,6698296200.0,22327654.0,D1 1.fq.gz,0:150 1:150,A:1843962508;C:1518208646;G:1509450148;T:1826674898;N:0,150,150,,,1843962508,1518208646,1509450148,1826674898,0,SRX28811681,SRS25048554,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36217,SRR33581825,SRX28811680,SRS25048553,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L7,,strain:Not collected|isolate:PN L7|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:6|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L7,PN L7,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B3_1.fq.gz B3_2.fq.gz,fastq fastq,6611023200.0,22036744.0,B3 1.fq.gz,0:150 1:150,A:1823488173;C:1492231000;G:1485521400;T:1809782627;N:0,150,150,,,1823488173,1492231000,1485521400,1809782627,0,SRX28811680,SRS25048553,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36218,SRR33581826,SRX28811679,SRS25048552,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L2,,strain:Not collected|isolate:PN L2|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L2,PN L2,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B2_1.fq.gz B2_2.fq.gz,fastq fastq,6673419600.0,22244732.0,B2 1.fq.gz,0:150 1:150,A:1853555661;C:1496204062;G:1487686506;T:1835973371;N:0,150,150,,,1853555661,1496204062,1487686506,1835973371,0,SRX28811679,SRS25048552,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36219,SRR33581827,SRX28811678,SRS25048551,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,PN L4,,strain:Not collected|isolate:PN L4|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Model,PN L4,PN L4,Model,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,B1_1.fq.gz B1_2.fq.gz,fastq fastq,6654915300.0,22183051.0,B1 1.fq.gz,0:150 1:150,A:1864666474;C:1477163584;G:1469026869;T:1844058373;N:0,150,150,,,1864666474,1477163584,1469026869,1844058373,0,SRX28811678,SRS25048551,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36220,SRR33581828,SRX28811677,SRS25048550,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con L1,,strain:Not collected|isolate:Con L1|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con L1,Con L1,Control,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A3_1.fq.gz A3_2.fq.gz,fastq fastq,6805948200.0,22686494.0,A3 1.fq.gz,0:150 1:150,A:1865806598;C:1548653255;G:1540767459;T:1850720888;N:0,150,150,,,1865806598,1548653255,1540767459,1850720888,0,SRX28811677,SRS25048550,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36221,SRR33581829,SRX28811676,SRS25048549,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con Lb,,strain:Not collected|isolate:Con Lb|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con Lb,Con Lb,Control,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A2_1.fq.gz A2_2.fq.gz,fastq fastq,6807123600.0,22690412.0,A2 1.fq.gz,0:150 1:150,A:1868554012;C:1546467202;G:1539322143;T:1852780243;N:0,150,150,,,1868554012,1546467202,1539322143,1852780243,0,SRX28811676,SRS25048549,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
36222,SRR33581830,SRX28811675,SRS25048548,SRP585544,PRJNA1263423,Ginsenoside Rg1 modulates key pathways in zebrafish with glucocorticoid induced osteoporosis,PRJNA1263423,Other,,,,,,Con La,,strain:Not collected|isolate:Con La|cultivar:Not collected|ecotype:Not collected|age:8 dpf stage:Larvae|collection date:2024 06 03|geo loc name:Not collected|sex:Not collected|tissue:Larvae|tmp:1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Zebrafish: Control,Con La,Con La,,,,WGS,TRANSCRIPTOMIC,PolyA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP585544,,,A1_1.fq.gz A1_2.fq.gz,fastq fastq,6782914200.0,22609714.0,A1 1.fq.gz,0:150 1:150,A:1857557307;C:1544915899;G:1537431564;T:1843009430;N:0,150,150,,,1857557307,1544915899,1537431564,1843009430,0,SRX28811675,SRS25048548,SRA2130283,Hubei University of Medicine|Graduate school,Hubei University of Medicine,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2025-05-15,Larval,Larval,Undetermined,Undetermined
59036,SRR11578951,SRX8146805,SRS6509417,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,WT,54WT4,54WT4,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT4 R1 001.fastq.gz|filename2:54WT4 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54WT4,S7,S7,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54WT4_R2_001.fastq.gz 54WT4_R1_001.fastq.gz,fastq fastq,7136583059.0,47328719.0,54WT4 R1 001.fastq.gz,0:75.39 1:75.40,A:1980254600;C:1593971374;G:1644375041;T:1916731613;N:1250431,75,75,,,1980254600,1593971374,1644375041,1916731613,1250431,SRX8146805,SRS6509417,SRA1067518,UPF|Genomics,UPF,2,0.91504,0.91439,0.09602,0.09527,0.73245,0.73777,0.46955,0.48655,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59037,SRR11578952,SRX8146804,SRS6509416,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,WT,54WT3,54WT3,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT3 R1 001.fastq.gz|filename2:54WT3 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54WT3,S5,S5,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54WT3_R1_001.fastq.gz 54WT3_R2_001.fastq.gz,fastq fastq,5683476624.0,37713746.0,54WT3 R1 001.fastq.gz,0:75.35 1:75.35,A:1578885174;C:1271523804;G:1309222456;T:1522827535;N:1017655,75,75,,,1578885174,1271523804,1309222456,1522827535,1017655,SRX8146804,SRS6509416,SRA1067518,UPF|Genomics,UPF,2,0.91126,0.91193,0.10356,0.10472,0.73975,0.7461,0.47619,0.47737,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59038,SRR11578953,SRX8146803,SRS6509415,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,WT,54WT2,54WT2,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT2 R1 001.fastq.gz|filename2:54WT2 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54WT2,S3,S3,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54WT2_R1_001.fastq.gz 54WT2_R2_001.fastq.gz,fastq fastq,6860136869.0,45523385.0,54WT2 R1 001.fastq.gz,0:75.34 1:75.35,A:1906640944;C:1530528609;G:1580010044;T:1841799217;N:1158055,75,75,,,1906640944,1530528609,1580010044,1841799217,1158055,SRX8146803,SRS6509415,SRA1067518,UPF|Genomics,UPF,2,0.91215,0.91207,0.10861,0.11028,0.74381,0.74968,0.48908,0.49262,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59039,SRR11578954,SRX8146802,SRS6509414,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,WT,54WT1,54WT1,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT1 R1 001.fastq.gz|filename2:54WT1 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54WT1,S1,S1,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54WT1_R1_001.fastq.gz 54WT1_R2_001.fastq.gz,fastq fastq,6225284142.0,41319897.0,54WT1 R1 001.fastq.gz,0:75.33 1:75.33,A:1729358086;C:1392766589;G:1430690093;T:1671396108;N:1073266,75,75,,,1729358086,1392766589,1430690093,1671396108,1073266,SRX8146802,SRS6509414,SRA1067518,UPF|Genomics,UPF,2,0.92733,0.92867,0.09387,0.09333,0.71163,0.71494,0.486,0.48867,72,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59040,SRR11578955,SRX8146801,SRS6509413,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,Clo,54Clo4,54Clo4,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo4 R1 001.fastq.gz|filename2:54Clo4 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54Clo4,S8,S8,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54Clo4_R1_001.fastq.gz 54Clo4_R2_001.fastq.gz,fastq fastq,6770856878.0,44915858.0,54Clo4 R1 001.fastq.gz,0:75.37 1:75.38,A:1876646232;C:1514408795;G:1561029116;T:1817557290;N:1215445,75,75,,,1876646232,1514408795,1561029116,1817557290,1215445,SRX8146801,SRS6509413,SRA1067518,UPF|Genomics,UPF,2,0.91659,0.91674,0.10388,0.10458,0.71948,0.72523,0.48917,0.4856,76,74,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59041,SRR11578956,SRX8146800,SRS6509412,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,Clo,54Clo3,54Clo3,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo3 R1 001.fastq.gz|filename2:54Clo3 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54Clo3,S6,S6,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54Clo3_R2_001.fastq.gz 54Clo3_R1_001.fastq.gz,fastq fastq,5822390786.0,38650567.0,54Clo3 R1 001.fastq.gz,0:75.32 1:75.32,A:1619353584;C:1299190067;G:1337336722;T:1565486844;N:1023569,75,75,,,1619353584,1299190067,1337336722,1565486844,1023569,SRX8146800,SRS6509412,SRA1067518,UPF|Genomics,UPF,2,0.91509,0.91425,0.10591,0.10604,0.76386,0.7693,0.46813,0.46524,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59042,SRR11578957,SRX8146799,SRS6509411,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,Clo,54Clo2,54Clo2,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo2 R1 001.fastq.gz|filename2:54Clo2 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54Clo2,S4,S4,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54Clo2_R2_001.fastq.gz 54Clo2_R1_001.fastq.gz,fastq fastq,6138626977.0,40727824.0,54Clo2 R1 001.fastq.gz,0:75.36 1:75.36,A:1700144556;C:1378599434;G:1420945150;T:1637894336;N:1043501,75,75,,,1700144556,1378599434,1420945150,1637894336,1043501,SRX8146799,SRS6509411,SRA1067518,UPF|Genomics,UPF,2,0.90602,0.90662,0.09596,0.09691,0.75872,0.76274,0.48174,0.48196,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise
59043,SRR11578958,SRX8146798,SRS6509410,SRP257662,PRJNA627095,Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf,PRJNA627095,Other,In many organs  stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels  however whether vasculature is an integral component of their niches is yet unknown. Here  two separate  novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead  requires blood flow to trigger a transcriptional response  which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether  we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.,,,Clo,54Clo1,54Clo1,,strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo1 R1 001.fastq.gz|filename2:54Clo1 R2 001.fastq.gz|BioSampleModel:Model organism or animal,,,,,,,,,54Clo1,S2,S2,low input mRNA sequencing,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP257662,,,54Clo1_R1_001.fastq.gz 54Clo1_R2_001.fastq.gz,fastq fastq,7414571165.0,49175642.0,54Clo1 R1 001.fastq.gz,0:75.39 1:75.39,A:2056892212;C:1660481957;G:1708780731;T:1987161426;N:1254839,75,75,,,2056892212,1660481957,1708780731,1987161426,1254839,SRX8146798,SRS6509410,SRA1067518,UPF|Genomics,UPF,2,0.90938,0.91029,0.1024,0.1024,0.73507,0.73852,0.48964,0.48917,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2020-04-21,Hatching,Embryo,Undetermined,Embryo Imprecise