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
288,DRR224554,DRX214839,DRS236362,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult C,SAMD00222585,,sample name:Adult C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222585,DRX214839,Adult C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222585,,,,11727505800.0,58637529.0,DRR224554,0:100 1:100,A:3137648588;C:2705013210;G:3191753451;T:2692963496;N:127055,100,100,,,3137648588,2705013210,3191753451,2692963496,127055,DRX214839,DRS236362,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95934,0.93156,0.03853,0.0394,0.72683,0.74625,0.45812,0.47098,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
289,DRR224553,DRX214838,DRS236361,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult B,SAMD00222584,,sample name:Adult B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222584,DRX214838,Adult B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222584,,,,22010855600.0,110054278.0,DRR224553,0:100 1:100,A:5511440112;C:5498539659;G:5546758172;T:5453879750;N:237907,100,100,,,5511440112,5498539659,5546758172,5453879750,237907,DRX214838,DRS236361,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95774,0.95394,0.04568,0.04411,0.70701,0.70881,0.47041,0.47938,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
290,DRR224552,DRX214837,DRS236360,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish Adult A,SAMD00222583,,sample name:Adult A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222583,DRX214837,Adult A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222583,,,,17683281000.0,88416405.0,DRR224552,0:100 1:100,A:4386756926;C:4479415938;G:4578796094;T:4238125580;N:186462,100,100,,,4386756926,4479415938,4578796094,4238125580,186462,DRX214837,DRS236360,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95974,0.95566,0.05237,0.05086,0.74357,0.74742,0.48578,0.49971,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Adult,Adult,Fin,Surface Structure
291,DRR224551,DRX214836,DRS236359,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf C,SAMD00222582,,sample name:42dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222582,DRX214836,42dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222582,,,,14328721000.0,71643605.0,DRR224551,0:100 1:100,A:3545040254;C:3629416092;G:3695002549;T:3459108561;N:153544,100,100,,,3545040254,3629416092,3695002549,3459108561,153544,DRX214836,DRS236359,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9671,0.95979,0.04174,0.04058,0.71867,0.72143,0.44818,0.46122,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
292,DRR224550,DRX214835,DRS236358,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf B,SAMD00222581,,sample name:42dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,DRX214835,42dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222581,,,,14782437000.0,73912185.0,DRR224550,0:100 1:100,A:3652595601;C:3746189790;G:3788229051;T:3595263949;N:158609,100,100,,,3652595601,3746189790,3788229051,3595263949,158609,DRX214835,DRS236358,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96502,0.95776,0.0417,0.0399,0.71311,0.71423,0.46064,0.44469,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
293,DRR224549,DRX214834,DRS236357,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 42dpf A,SAMD00222580,,sample name:42dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,DRX214834,42dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222580,,,,17895751600.0,89478758.0,DRR224549,0:100 1:100,A:4428562207;C:4525140210;G:4573827895;T:4368029340;N:191948,100,100,,,4428562207,4525140210,4573827895,4368029340,191948,DRX214834,DRS236357,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96506,0.96043,0.04654,0.0446,0.70956,0.71153,0.49143,0.48957,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Juvenile,Juvenile,Fin,Surface Structure
294,DRR224548,DRX214833,DRS236356,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf C,SAMD00222579,,sample name:28dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222579,DRX214833,28dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222579,,,,16269568600.0,81347843.0,DRR224548,0:100 1:100,A:3978004953;C:4160626131;G:4174223034;T:3956539398;N:175084,100,100,,,3978004953,4160626131,4174223034,3956539398,175084,DRX214833,DRS236356,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9633,0.95842,0.0474,0.04564,0.72184,0.72253,0.47871,0.46471,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
295,DRR224547,DRX214832,DRS236355,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf B,SAMD00222578,,sample name:28dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222578,DRX214832,28dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222578,,,,19970979800.0,99854899.0,DRR224547,0:100 1:100,A:5064043525;C:4909415172;G:5303813974;T:4693498507;N:208622,100,100,,,5064043525,4909415172,5303813974,4693498507,208622,DRX214832,DRS236355,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.95486,0.94587,0.05718,0.05404,0.73746,0.74754,0.51956,0.47088,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
296,DRR224546,DRX214831,DRS236354,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 28dpf A,SAMD00222577,,sample name:28dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222577,DRX214831,28dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222577,,,,17870876400.0,89354382.0,DRR224546,0:100 1:100,A:4431724830;C:4512913394;G:4543413766;T:4382632384;N:192026,100,100,,,4431724830,4512913394,4543413766,4382632384,192026,DRX214831,DRS236354,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9608,0.95643,0.045,0.04296,0.7236,0.7234,0.50029,0.50287,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
297,DRR224545,DRX214830,DRS236353,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf C,SAMD00222576,,sample name:14dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222576,DRX214830,14dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222576,,,,16979810200.0,84899051.0,DRR224545,0:100 1:100,A:4241907225;C:4256915446;G:4277991608;T:4202813567;N:182354,100,100,,,4241907225,4256915446,4277991608,4202813567,182354,DRX214830,DRS236353,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96662,0.96168,0.03768,0.03562,0.72368,0.72464,0.48494,0.48687,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
298,DRR224544,DRX214829,DRS236352,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf B,SAMD00222575,,sample name:14dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222575,DRX214829,14dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222575,,,,18273780000.0,91368900.0,DRR224544,0:100 1:100,A:4545336763;C:4589502978;G:4635310325;T:4503435996;N:193938,100,100,,,4545336763,4589502978,4635310325,4503435996,193938,DRX214829,DRS236352,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97073,0.96595,0.03063,0.02973,0.73632,0.73758,0.47494,0.46918,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
299,DRR224543,DRX214828,DRS236351,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 14dpf A,SAMD00222574,,sample name:14dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222574,DRX214828,14dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222574,,,,18294607600.0,91473038.0,DRR224543,0:100 1:100,A:4623135433;C:4539347940;G:4561846652;T:4570079366;N:198209,100,100,,,4623135433,4539347940,4561846652,4570079366,198209,DRX214828,DRS236351,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96261,0.9592,0.02999,0.02873,0.72699,0.72796,0.4679,0.46591,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
300,DRR224542,DRX214827,DRS236350,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf C,SAMD00222573,,sample name:5dpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222573,DRX214827,5dpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222573,,,,18736996000.0,93684980.0,DRR224542,0:100 1:100,A:4647244376;C:4733187951;G:4746515898;T:4609906214;N:141561,100,100,,,4647244376,4733187951,4746515898,4609906214,141561,DRX214827,DRS236350,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97229,0.96893,0.042,0.03995,0.74172,0.74328,0.44607,0.44755,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
301,DRR224541,DRX214826,DRS236349,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf B,SAMD00222572,,sample name:5dpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222572,DRX214826,5dpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222572,,,,22151021400.0,110755107.0,DRR224541,0:100 1:100,A:5555093734;C:5532777660;G:5592525988;T:5470461779;N:162239,100,100,,,5555093734,5532777660,5592525988,5470461779,162239,DRX214826,DRS236349,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96835,0.96645,0.04001,0.03872,0.72865,0.72934,0.46355,0.46428,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
302,DRR224540,DRX214825,DRS236348,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin from RIKEN Wild type zebrafish at 5dpf A,SAMD00222571,,sample name:5dpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222571,DRX214825,5dpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222571,,,,18219864200.0,91099321.0,DRR224540,0:100 1:100,A:4485880313;C:4629712312;G:4617351502;T:4486786107;N:133966,100,100,,,4485880313,4629712312,4617351502,4486786107,133966,DRX214825,DRS236348,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97075,0.96902,0.04498,0.0432,0.72971,0.73044,0.45267,0.4604,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Larval,Larval,Fin,Surface Structure
303,DRR224539,DRX214824,DRS236347,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 48hpf C,SAMD00222570,,sample name:48hpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222570,DRX214824,48hpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222570,,,,16828182200.0,84140911.0,DRR224539,0:100 1:100,A:3957959900;C:4467368792;G:4483580218;T:3919146988;N:126302,100,100,,,3957959900,4467368792,4483580218,3919146988,126302,DRX214824,DRS236347,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97277,0.97115,0.05409,0.05185,0.76717,0.76836,0.46592,0.45571,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Hatching,Embryo,Fin,Surface Structure
304,DRR224538,DRX214823,DRS236346,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 48hpf B,SAMD00222569,,sample name:48hpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222569,DRX214823,48hpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222569,,,,22815822200.0,114079111.0,DRR224538,0:100 1:100,A:5651922913;C:5760379580;G:5844694518;T:5558658503;N:166686,100,100,,,5651922913,5760379580,5844694518,5558658503,166686,DRX214823,DRS236346,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96814,0.96379,0.03526,0.03362,0.71575,0.71697,0.47605,0.47359,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Hatching,Embryo,Fin,Surface Structure
305,DRR224537,DRX214822,DRS236345,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 48hpf A,SAMD00222568,,sample name:48hpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222568,DRX214822,48hpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222568,,,,13993230400.0,69966152.0,DRR224537,0:100 1:100,A:3484590137;C:3511805255;G:3624285719;T:3372446706;N:102583,100,100,,,3484590137,3511805255,3624285719,3372446706,102583,DRX214822,DRS236345,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96467,0.96428,0.04367,0.04212,0.72853,0.73125,0.49715,0.49652,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Hatching,Embryo,Fin,Surface Structure
306,DRR224536,DRX214821,DRS236344,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf C,SAMD00222567,,sample name:40hpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222567,DRX214821,40hpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222567,,,,14926054400.0,74630272.0,DRR224536,0:100 1:100,A:3647365116;C:3826172690;G:3866071867;T:3586333511;N:111216,100,100,,,3647365116,3826172690,3866071867,3586333511,111216,DRX214821,DRS236344,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96395,0.96168,0.05081,0.04957,0.75489,0.75607,0.51046,0.52135,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
307,DRR224535,DRX214820,DRS236343,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf B,SAMD00222566,,sample name:40hpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222566,DRX214820,40hpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222566,,,,14413995800.0,72069979.0,DRR224535,0:100 1:100,A:3598207137;C:3642219692;G:3750145663;T:3423315835;N:107473,100,100,,,3598207137,3642219692,3750145663,3423315835,107473,DRX214820,DRS236343,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97396,0.97107,0.04686,0.04549,0.7444,0.74968,0.50051,0.49798,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
308,DRR224534,DRX214819,DRS236342,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 40hpf A,SAMD00222565,,sample name:40hpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222565,DRX214819,40hpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222565,,,,14351831800.0,71759159.0,DRR224534,0:100 1:100,A:3552114377;C:3639389412;G:3719404253;T:3440817088;N:106670,100,100,,,3552114377,3639389412,3719404253,3440817088,106670,DRX214819,DRS236342,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.96606,0.96569,0.04249,0.04107,0.7514,0.75367,0.49762,0.49753,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
309,DRR224533,DRX214818,DRS236341,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf C,SAMD00222564,,sample name:32hpf C,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222564,DRX214818,32hpf C,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222564,,,,18499667800.0,92498339.0,DRR224533,0:100 1:100,A:4655671152;C:4605325822;G:4688156846;T:4550378341;N:135639,100,100,,,4655671152,4605325822,4688156846,4550378341,135639,DRX214818,DRS236341,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.9673,0.96864,0.04184,0.04008,0.73087,0.73318,0.48331,0.48043,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
310,DRR224532,DRX214817,DRS236340,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf B,SAMD00222563,,sample name:32hpf B,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222563,DRX214817,32hpf B,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222563,,,,19952418000.0,99762090.0,DRR224532,0:100 1:100,A:4972665902;C:5012518349;G:5094132814;T:4872951533;N:149402,100,100,,,4972665902,5012518349,5094132814,4872951533,149402,DRX214817,DRS236340,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97325,0.97252,0.03729,0.03575,0.71591,0.7163,0.47191,0.47859,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
311,DRR224531,DRX214816,DRS236339,DRP008458,PRJDB9741,RNA seq for developing pectoral fin in zebrafish,DRP008458,Other,From the developmental view of fin to limb transition  an important event in vertebrate evolution  we seek fish specific genes that show characteristic expression pattern in the developing fin.,,,,pectoral fin bud from gM1116A zebrafish at 32hpf A,SAMD00222562,,sample name:32hpf A,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00222562,DRX214816,32hpf A,1,Illumina TruSeq Stranded mRNA Library Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP008458,Illumina NovaSeq 6000 paired end sequencing of SAMD00222562,,,,16357024800.0,81785124.0,DRR224531,0:100 1:100,A:4049805675;C:4130985751;G:4172952730;T:4003159212;N:121432,100,100,,,4049805675,4130985751,4172952730,4003159212,121432,DRX214816,DRS236339,DRA010086,TOHOKUGL|Laboratory of organ morphogenesis,"Graduate School of Life Sciences, Tohoku University",2,0.97046,0.96886,0.03577,0.03489,0.73257,0.73231,0.4825,0.48849,100,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Japan,2022-04-21,Pharyngula,Embryo,Fin,Surface Structure
7898,ERR3446778,ERX3468777,ERS1806709,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A7,SAMEA104147691,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147691|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a44a000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a44a000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934993,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#48,DN488439N:H6,Illumina sequencing of library DN488439N:H6  constructed from sample accession ERS1806709 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTCAGCTC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#48.cram,cram,308695200.0,2057968.0,SC RUN 22829 8#48,0:75 1:75,A:81122866;C:71193244;G:71997258;T:83822324;N:559508,75,75,,,81122866,71193244,71997258,83822324,559508,ERX3468777,ERS1806709,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.89599,0.93164,0.14865,0.15283,0.69217,0.69759,0.50417,0.50646,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7899,ERR3446777,ERX3468776,ERS1806708,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A10,SAMEA104147690,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147690|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a397c70 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a397c70 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934992,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#47,DN488439N:G6,Illumina sequencing of library DN488439N:G6  constructed from sample accession ERS1806708 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TACTAGTC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#47.cram,cram,995580450.0,6637203.0,SC RUN 22829 8#47,0:75 1:75,A:262413326;C:232761029;G:232382381;T:266176133;N:1847581,75,75,,,262413326,232761029,232382381,266176133,1847581,ERX3468776,ERS1806708,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95746,0.96146,0.13411,0.13002,0.69954,0.70128,0.51593,0.51584,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7900,ERR3446776,ERX3468775,ERS1806707,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A5,SAMEA104147689,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147689|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a2b4ba0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a2b4ba0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934991,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#46,DN488439N:F6,Illumina sequencing of library DN488439N:F6  constructed from sample accession ERS1806707 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCAGATTC.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#46.cram,cram,802088550.0,5347257.0,SC RUN 22829 8#46,0:75 1:75,A:215471665;C:183766661;G:183444943;T:217939641;N:1465640,75,75,,,215471665,183766661,183444943,217939641,1465640,ERX3468775,ERS1806707,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95288,0.95668,0.16762,0.16588,0.68785,0.6896,0.51555,0.51471,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7901,ERR3446775,ERX3468774,ERS1806706,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E7,SAMEA104147688,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147688|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a207630 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a207630 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934990,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#45,DN488439N:E6,Illumina sequencing of library DN488439N:E6  constructed from sample accession ERS1806706 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TATGCCAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#45.cram,cram,895634850.0,5970899.0,SC RUN 22829 8#45,0:75 1:75,A:237133265;C:208424547;G:207465996;T:240955635;N:1655407,75,75,,,237133265,208424547,207465996,240955635,1655407,ERX3468774,ERS1806706,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95242,0.95616,0.148,0.14527,0.68166,0.68489,0.49334,0.49766,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7902,ERR3446774,ERX3468773,ERS1806705,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D5,SAMEA104147687,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147687|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a15a0c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a15a0c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934989,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#44,DN488439N:D6,Illumina sequencing of library DN488439N:D6  constructed from sample accession ERS1806705 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGGCTCAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#44.cram,cram,897162300.0,5981082.0,SC RUN 22829 8#44,0:75 1:75,A:236623845;C:209590114;G:209138794;T:240168869;N:1640678,75,75,,,236623845,209590114,209138794,240168869,1640678,ERX3468773,ERS1806705,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95642,0.95978,0.15673,0.15393,0.68941,0.69298,0.50945,0.51331,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7903,ERR3446773,ERX3468772,ERS1806704,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B9,SAMEA104147686,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147686|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:3a0acb50 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3a0acb50 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934988,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#43,DN488439N:C6,Illumina sequencing of library DN488439N:C6  constructed from sample accession ERS1806704 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCATTGAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#43.cram,cram,1041347100.0,6942314.0,SC RUN 22829 8#43,0:75 1:75,A:275192375;C:242588569;G:242047235;T:279597410;N:1921511,75,75,,,275192375,242588569,242047235,279597410,1921511,ERX3468772,ERS1806704,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95538,0.95935,0.12658,0.12175,0.68527,0.68594,0.49686,0.49869,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7904,ERR3446772,ERX3468771,ERS1806703,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A9,SAMEA104147685,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147685|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:39fff5e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39fff5e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934987,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#42,DN488439N:B6,Illumina sequencing of library DN488439N:B6  constructed from sample accession ERS1806703 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGTATGCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#42.cram,cram,1003046550.0,6686977.0,SC RUN 22829 8#42,0:75 1:75,A:264604462;C:234287668;G:233610516;T:268704610;N:1839294,75,75,,,264604462,234287668,233610516,268704610,1839294,ERX3468771,ERS1806703,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9545,0.95817,0.14837,0.14477,0.69075,0.69477,0.5059,0.50954,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7905,ERR3446771,ERX3468770,ERS1806702,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D1,SAMEA104147684,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147684|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:32Z|INSDC status:public|Submitter Id:39f52070 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39f52070 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934986,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#41,DN488439N:A6,Illumina sequencing of library DN488439N:A6  constructed from sample accession ERS1806702 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCCAGTCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#41.cram,cram,941981400.0,6279876.0,SC RUN 22829 8#41,0:75 1:75,A:246347736;C:221993645;G:222033599;T:249879875;N:1726545,75,75,,,246347736,221993645,222033599,249879875,1726545,ERX3468770,ERS1806702,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95497,0.95862,0.14626,0.14366,0.68069,0.68219,0.51091,0.5108,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7906,ERR3446770,ERX3468769,ERS1806701,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 F3,SAMEA104147683,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147683|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39ea4b00 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39ea4b00 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934985,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#40,DN488439N:H5,Illumina sequencing of library DN488439N:H5  constructed from sample accession ERS1806701 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAAGTTCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#40.cram,cram,943793700.0,6291958.0,SC RUN 22829 8#40,0:75 1:75,A:248418195;C:220858029;G:220899307;T:251893736;N:1724433,75,75,,,248418195,220858029,220899307,251893736,1724433,ERX3468769,ERS1806701,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95501,0.95869,0.15165,0.15013,0.6858,0.68968,0.51097,0.51107,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7907,ERR3446769,ERX3468768,ERS1806700,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A12,SAMEA104147682,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147682|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39df7590 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39df7590 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934984,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#39,DN488439N:G5,Illumina sequencing of library DN488439N:G5  constructed from sample accession ERS1806700 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCAGGAGG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#39.cram,cram,1013740350.0,6758269.0,SC RUN 22829 8#39,0:75 1:75,A:272175825;C:231609775;G:230992859;T:277093551;N:1868340,75,75,,,272175825,231609775,230992859,277093551,1868340,ERX3468768,ERS1806700,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95017,0.95405,0.17783,0.17326,0.69374,0.69792,0.52105,0.52106,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7908,ERR3446768,ERX3468767,ERS1806699,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A8,SAMEA104147681,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147681|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39d4a020 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39d4a020 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934983,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#38,DN488439N:F5,Illumina sequencing of library DN488439N:F5  constructed from sample accession ERS1806699 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCTCACGG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#38.cram,cram,795064350.0,5300429.0,SC RUN 22829 8#38,0:75 1:75,A:213296717;C:181969652;G:181448689;T:216888172;N:1461120,75,75,,,213296717,181969652,181448689,216888172,1461120,ERX3468767,ERS1806699,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95132,0.955,0.15976,0.15558,0.68483,0.68828,0.50493,0.50817,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7909,ERR3446767,ERX3468766,ERS1806698,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D8,SAMEA104147680,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147680|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39c9cab0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39c9cab0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934982,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#37,DN488439N:E5,Illumina sequencing of library DN488439N:E5  constructed from sample accession ERS1806698 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TACTTCGG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#37.cram,cram,977579400.0,6517196.0,SC RUN 22829 8#37,0:75 1:75,A:259910020;C:226288538;G:225374569;T:264216059;N:1790214,75,75,,,259910020,226288538,225374569,264216059,1790214,ERX3468766,ERS1806698,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95353,0.95725,0.15221,0.14901,0.68442,0.6873,0.48878,0.49948,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7910,ERR3446766,ERX3468765,ERS1806697,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D9,SAMEA104147679,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147679|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39bece30 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39bece30 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934981,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#36,DN488439N:D5,Illumina sequencing of library DN488439N:D5  constructed from sample accession ERS1806697 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGAACTGG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#36.cram,cram,936668850.0,6244459.0,SC RUN 22829 8#36,0:75 1:75,A:249181628;C:216639604;G:216150821;T:252967247;N:1729550,75,75,,,249181628,216639604,216150821,252967247,1729550,ERX3468765,ERS1806697,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95513,0.95852,0.15768,0.15381,0.68438,0.68799,0.51177,0.50632,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7911,ERR3446765,ERX3468764,ERS1806696,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C1,SAMEA104147678,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147678|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:31Z|INSDC status:public|Submitter Id:39b3f8c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39b3f8c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934980,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#35,DN488439N:C5,Illumina sequencing of library DN488439N:C5  constructed from sample accession ERS1806696 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTGGTATG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#35.cram,cram,975853650.0,6505691.0,SC RUN 22829 8#35,0:75 1:75,A:258866840;C:226232975;G:225877015;T:263074733;N:1802087,75,75,,,258866840,226232975,225877015,263074733,1802087,ERX3468764,ERS1806696,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95586,0.9586,0.14753,0.14367,0.68964,0.69345,0.50825,0.50489,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7912,ERR3446764,ERX3468763,ERS1806694,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E5,SAMEA104147676,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147676|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:39a74e90 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39a74e90 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934979,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#34,DN488439N:B5,Illumina sequencing of library DN488439N:B5  constructed from sample accession ERS1806694 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAACGCTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#34.cram,cram,960618450.0,6404123.0,SC RUN 22829 8#34,0:75 1:75,A:252530928;C:225220073;G:224701067;T:256397819;N:1768563,75,75,,,252530928,225220073,224701067,256397819,1768563,ERX3468763,ERS1806694,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95621,0.95933,0.15326,0.15001,0.68278,0.68574,0.50498,0.50559,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7913,ERR3446763,ERX3468762,ERS1806693,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D11,SAMEA104147675,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147675|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:399c7920 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:399c7920 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934978,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#33,DN488439N:A5,Illumina sequencing of library DN488439N:A5  constructed from sample accession ERS1806693 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCGAAGTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#33.cram,cram,1038077400.0,6920516.0,SC RUN 22829 8#33,0:75 1:75,A:270310565;C:245873612;G:245834117;T:274135301;N:1923805,75,75,,,270310565,245873612,245834117,274135301,1923805,ERX3468762,ERS1806693,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9563,0.96046,0.13363,0.13125,0.67858,0.68095,0.49926,0.4941,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7914,ERR3446762,ERX3468761,ERS1806695,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A1,SAMEA104147677,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147677|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:39901d10 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39901d10 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934977,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#32,DN488439N:H4,Illumina sequencing of library DN488439N:H4  constructed from sample accession ERS1806695 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTCCATTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#32.cram,cram,986612850.0,6577419.0,SC RUN 22829 8#32,0:75 1:75,A:259827485;C:230648413;G:231077889;T:263216608;N:1842455,75,75,,,259827485,230648413,231077889,263216608,1842455,ERX3468761,ERS1806695,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95392,0.95801,0.15749,0.15741,0.68633,0.68941,0.51453,0.5162,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7915,ERR3446761,ERX3468760,ERS1806691,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B1,SAMEA104147673,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147673|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:398547a0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:398547a0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934976,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#31,DN488439N:G4,Illumina sequencing of library DN488439N:G4  constructed from sample accession ERS1806691 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAGTCTTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#31.cram,cram,1031442450.0,6876283.0,SC RUN 22829 8#31,0:75 1:75,A:274203878;C:238375461;G:238376358;T:278589476;N:1897277,75,75,,,274203878,238375461,238376358,278589476,1897277,ERX3468760,ERS1806691,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95118,0.95551,0.16324,0.16064,0.68615,0.68925,0.51221,0.50738,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7916,ERR3446760,ERX3468759,ERS1806692,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B8,SAMEA104147674,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147674|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:397a9940 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:397a9940 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934975,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#30,DN488439N:F4,Illumina sequencing of library DN488439N:F4  constructed from sample accession ERS1806692 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGTGGTTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#30.cram,cram,841629750.0,5610865.0,SC RUN 22829 8#30,0:75 1:75,A:224237300;C:194199747;G:193893668;T:227725985;N:1573050,75,75,,,224237300,194199747,193893668,227725985,1573050,ERX3468759,ERS1806692,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95236,0.95666,0.15496,0.1528,0.68049,0.68406,0.50292,0.50201,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7917,ERR3446759,ERX3468758,ERS1806690,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C3,SAMEA104147672,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147672|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:396fc3d0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:396fc3d0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934974,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#29,DN488439N:E4,Illumina sequencing of library DN488439N:E4  constructed from sample accession ERS1806690 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCCTCAAT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#29.cram,cram,1003675800.0,6691172.0,SC RUN 22829 8#29,0:75 1:75,A:267034518;C:232079842;G:231287862;T:271430075;N:1843503,75,75,,,267034518,232079842,231287862,271430075,1843503,ERX3468758,ERS1806690,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95315,0.9573,0.15329,0.151,0.6869,0.68911,0.49176,0.49755,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7918,ERR3446758,ERX3468757,ERS1806689,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A2,SAMEA104147671,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147671|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:3962a470 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3962a470 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934973,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#28,DN488439N:D4,Illumina sequencing of library DN488439N:D4  constructed from sample accession ERS1806689 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TACAGGAT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#28.cram,cram,877026750.0,5846845.0,SC RUN 22829 8#28,0:75 1:75,A:234056953;C:201909571;G:201550258;T:237878368;N:1631600,75,75,,,234056953,201909571,201550258,237878368,1631600,ERX3468757,ERS1806689,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95174,0.95506,0.16448,0.1594,0.68696,0.68956,0.51105,0.51529,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7919,ERR3446757,ERX3468756,ERS1806688,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B7,SAMEA104147670,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147670|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:3957cf00 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3957cf00 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934972,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#27,DN488439N:C4,Illumina sequencing of library DN488439N:C4  constructed from sample accession ERS1806688 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAGTGACT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#27.cram,cram,976188150.0,6507921.0,SC RUN 22829 8#27,0:75 1:75,A:258533450;C:226872670;G:226382560;T:262604964;N:1794506,75,75,,,258533450,226872670,226382560,262604964,1794506,ERX3468756,ERS1806688,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95189,0.95679,0.13942,0.13618,0.68274,0.68505,0.50235,0.50513,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7920,ERR3446756,ERX3468755,ERS1806687,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B2,SAMEA104147669,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147669|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:30Z|INSDC status:public|Submitter Id:394a8890 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:394a8890 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934971,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#26,DN488439N:B4,Illumina sequencing of library DN488439N:B4  constructed from sample accession ERS1806687 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTCCTGCT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#26.cram,cram,893242800.0,5954952.0,SC RUN 22829 8#26,0:75 1:75,A:233780534;C:210342200;G:210386139;T:237085352;N:1648575,75,75,,,233780534,210342200,210386139,237085352,1648575,ERX3468755,ERS1806687,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9547,0.95931,0.14551,0.14251,0.68605,0.6871,0.51109,0.51231,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7921,ERR3446755,ERX3468754,ERS1806686,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D6,SAMEA104147668,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147668|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:393fb320 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:393fb320 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934970,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#25,DN488439N:A4,Illumina sequencing of library DN488439N:A4  constructed from sample accession ERS1806686 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGCGATCT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#25.cram,cram,990960750.0,6606405.0,SC RUN 22829 8#25,0:75 1:75,A:256751586;C:236231048;G:236105966;T:260051730;N:1820420,75,75,,,256751586,236231048,236105966,260051730,1820420,ERX3468754,ERS1806686,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95946,0.96347,0.13307,0.13209,0.68217,0.68505,0.4931,0.50013,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7922,ERR3446754,ERX3468753,ERS1806685,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E12,SAMEA104147667,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147667|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3931f780 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3931f780 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934969,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#24,DN488439N:H3,Illumina sequencing of library DN488439N:H3  constructed from sample accession ERS1806685 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTGACTCT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#24.cram,cram,964485000.0,6429900.0,SC RUN 22829 8#24,0:75 1:75,A:251451665;C:228331952;G:228439906;T:254469084;N:1792393,75,75,,,251451665,228331952,228439906,254469084,1792393,ERX3468753,ERS1806685,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9564,0.96106,0.12973,0.12899,0.67876,0.68254,0.49322,0.4891,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7923,ERR3446753,ERX3468752,ERS1806684,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D4,SAMEA104147666,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147666|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:39272210 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:39272210 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934968,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#23,DN488439N:G3,Illumina sequencing of library DN488439N:G3  constructed from sample accession ERS1806684 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGCATAGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#23.cram,cram,964272000.0,6428480.0,SC RUN 22829 8#23,0:75 1:75,A:251105580;C:228453524;G:228253397;T:254687699;N:1771800,75,75,,,251105580,228453524,228253397,254687699,1771800,ERX3468752,ERS1806684,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95716,0.96163,0.14819,0.14629,0.69016,0.69378,0.50746,0.51427,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7924,ERR3446752,ERX3468751,ERS1806683,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A3,SAMEA104147665,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147665|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:391c4ca0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:391c4ca0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934967,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#22,DN488439N:F3,Illumina sequencing of library DN488439N:F3  constructed from sample accession ERS1806683 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGATACGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#22.cram,cram,799230000.0,5328200.0,SC RUN 22829 8#22,0:75 1:75,A:212348969;C:184890796;G:184847246;T:215676416;N:1466573,75,75,,,212348969,184890796,184847246,215676416,1466573,ERX3468751,ERS1806683,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95436,0.95813,0.16036,0.1592,0.68759,0.69027,0.51144,0.50841,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7925,ERR3446751,ERX3468750,ERS1806681,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B6,SAMEA104147663,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147663|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3910b3e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3910b3e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934966,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#21,DN488439N:E3,Illumina sequencing of library DN488439N:E3  constructed from sample accession ERS1806681 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCGAGCGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#21.cram,cram,923983200.0,6159888.0,SC RUN 22829 8#21,0:75 1:75,A:243217021;C:216142090;G:216007590;T:246916174;N:1700325,75,75,,,243217021,216142090,216007590,246916174,1700325,ERX3468750,ERS1806681,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95874,0.96248,0.14485,0.14306,0.69633,0.69877,0.5064,0.50544,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7926,ERR3446750,ERX3468749,ERS1806682,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B10,SAMEA104147664,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147664|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:3905b760 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3905b760 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934965,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#20,DN488439N:D3,Illumina sequencing of library DN488439N:D3  constructed from sample accession ERS1806682 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTGGAGGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#20.cram,cram,896749650.0,5978331.0,SC RUN 22829 8#20,0:75 1:75,A:236504641;C:209373052;G:209286381;T:239943497;N:1642079,75,75,,,236504641,209373052,209286381,239943497,1642079,ERX3468749,ERS1806682,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95456,0.9591,0.14445,0.14205,0.68544,0.68809,0.50085,0.50894,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7927,ERR3446749,ERX3468748,ERS1806680,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C7,SAMEA104147662,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147662|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:29Z|INSDC status:public|Submitter Id:38fae1f0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38fae1f0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934964,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#19,DN488439N:C3,Illumina sequencing of library DN488439N:C3  constructed from sample accession ERS1806680 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCTGCTGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#19.cram,cram,933815700.0,6225438.0,SC RUN 22829 8#19,0:75 1:75,A:244718120;C:219569356;G:219612527;T:248215417;N:1700280,75,75,,,244718120,219569356,219612527,248215417,1700280,ERX3468748,ERS1806680,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95407,0.95781,0.14211,0.14014,0.68142,0.6845,0.5066,0.5032,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7928,ERR3446748,ERX3468747,ERS1806678,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A11,SAMEA104147660,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147660|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38f00c80 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38f00c80 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934963,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#18,DN488439N:B3,Illumina sequencing of library DN488439N:B3  constructed from sample accession ERS1806678 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTCTGTGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#18.cram,cram,905329500.0,6035530.0,SC RUN 22829 8#18,0:75 1:75,A:240021393;C:210015428;G:210218903;T:243401797;N:1671979,75,75,,,240021393,210015428,210218903,243401797,1671979,ERX3468747,ERS1806678,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95212,0.95525,0.15692,0.15381,0.68254,0.68525,0.52037,0.5208,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7929,ERR3446747,ERX3468746,ERS1806679,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E3,SAMEA104147661,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147661|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38e51000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38e51000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934962,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#17,DN488439N:A3,Illumina sequencing of library DN488439N:A3  constructed from sample accession ERS1806679 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGTACCTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#17.cram,cram,947665500.0,6317770.0,SC RUN 22829 8#17,0:75 1:75,A:246559305;C:224934978;G:224812411;T:249601963;N:1756843,75,75,,,246559305,224934978,224812411,249601963,1756843,ERX3468746,ERS1806679,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95666,0.96095,0.14463,0.14314,0.68757,0.68885,0.51144,0.51225,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7930,ERR3446746,ERX3468745,ERS1806677,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B4,SAMEA104147659,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147659|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38da3a90 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38da3a90 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934961,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#16,DN488439N:H2,Illumina sequencing of library DN488439N:H2  constructed from sample accession ERS1806677 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCCGTCTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#16.cram,cram,1017363750.0,6782425.0,SC RUN 22829 8#16,0:75 1:75,A:265624052;C:240509411;G:240546256;T:268829904;N:1854127,75,75,,,265624052,240509411,240546256,268829904,1854127,ERX3468745,ERS1806677,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95466,0.95911,0.14109,0.13929,0.68199,0.68262,0.49544,0.4999,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7931,ERR3446745,ERX3468744,ERS1806676,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D3,SAMEA104147658,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147658|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38c8d570 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38c8d570 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934960,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#15,DN488439N:G2,Illumina sequencing of library DN488439N:G2  constructed from sample accession ERS1806676 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAAGCGTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#15.cram,cram,1000345500.0,6668970.0,SC RUN 22829 8#15,0:75 1:75,A:258884239;C:238639192;G:238825356;T:262142988;N:1853725,75,75,,,258884239,238639192,238825356,262142988,1853725,ERX3468744,ERS1806676,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95861,0.96266,0.13649,0.13563,0.68755,0.69098,0.49977,0.50834,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7932,ERR3446744,ERX3468743,ERS1806675,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D7,SAMEA104147657,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147657|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38be0000 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38be0000 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934959,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#14,DN488439N:F2,Illumina sequencing of library DN488439N:F2  constructed from sample accession ERS1806675 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TCTCGGTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#14.cram,cram,831508200.0,5543388.0,SC RUN 22829 8#14,0:75 1:75,A:216944404;C:196565581;G:196615479;T:219853985;N:1528751,75,75,,,216944404,196565581,196615479,219853985,1528751,ERX3468743,ERS1806675,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95565,0.95932,0.13261,0.13138,0.67724,0.67971,0.49732,0.50908,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7933,ERR3446743,ERX3468742,ERS1806674,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C6,SAMEA104147656,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147656|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38b39fc0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38b39fc0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934958,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#13,DN488439N:E2,Illumina sequencing of library DN488439N:E2  constructed from sample accession ERS1806674 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGGTTGTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#13.cram,cram,880251450.0,5868343.0,SC RUN 22829 8#13,0:75 1:75,A:230018306;C:207962954;G:207702793;T:232909633;N:1657764,75,75,,,230018306,207962954,207702793,232909633,1657764,ERX3468742,ERS1806674,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95442,0.95837,0.12979,0.12922,0.6762,0.68081,0.49384,0.49413,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7934,ERR3446742,ERX3468741,ERS1806673,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C9,SAMEA104147655,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147655|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38aa29e0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38aa29e0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934957,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#12,DN488439N:D2,Illumina sequencing of library DN488439N:D2  constructed from sample accession ERS1806673 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence CTTGTACT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#12.cram,cram,885733500.0,5904890.0,SC RUN 22829 8#12,0:75 1:75,A:231281663;C:209310630;G:209302780;T:234229805;N:1608622,75,75,,,231281663,209310630,209302780,234229805,1608622,ERX3468741,ERS1806673,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95605,0.96017,0.13822,0.13754,0.68069,0.68385,0.50267,0.5053,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7935,ERR3446741,ERX3468740,ERS1806672,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B12,SAMEA104147654,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147654|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:28Z|INSDC status:public|Submitter Id:38a03ed0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38a03ed0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934956,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#11,DN488439N:C2,Illumina sequencing of library DN488439N:C2  constructed from sample accession ERS1806672 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence GGCTACAG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#11.cram,cram,836620350.0,5577469.0,SC RUN 22829 8#11,0:75 1:75,A:219115747;C:196807550;G:197091855;T:222058678;N:1546520,75,75,,,219115747,196807550,197091855,222058678,1546520,ERX3468740,ERS1806672,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95466,0.95919,0.15021,0.14856,0.69043,0.69244,0.50929,0.51567,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7936,ERR3446740,ERX3468739,ERS1806670,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E2,SAMEA104147652,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147652|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:38908760 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38908760 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934955,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#10,DN488439N:B2,Illumina sequencing of library DN488439N:B2  constructed from sample accession ERS1806670 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TAGCTTGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#10.cram,cram,911744850.0,6078299.0,SC RUN 22829 8#10,0:75 1:75,A:237470738;C:216053868;G:216099189;T:240450404;N:1670651,75,75,,,237470738,216053868,216099189,240450404,1670651,ERX3468739,ERS1806670,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95716,0.96092,0.14455,0.14187,0.68686,0.68954,0.50635,0.50911,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7937,ERR3446739,ERX3468738,ERS1806671,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C12,SAMEA104147653,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147653|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:3886c360 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3886c360 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934954,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#9,DN488439N:A2,Illumina sequencing of library DN488439N:A2  constructed from sample accession ERS1806671 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence GATCAGCG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#9.cram,cram,928894050.0,6192627.0,SC RUN 22829 8#9,0:75 1:75,A:243727946;C:218420567;G:218359552;T:246701233;N:1684752,75,75,,,243727946,218420567,218359552,246701233,1684752,ERX3468738,ERS1806671,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.9532,0.95745,0.14809,0.14652,0.68627,0.68911,0.5112,0.51053,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7938,ERR3446738,ERX3468737,ERS1806669,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B5,SAMEA104147651,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147651|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:387c1500 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:387c1500 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934953,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#8,DN488439N:H1,Illumina sequencing of library DN488439N:H1  constructed from sample accession ERS1806669 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence ACTTGATG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#8.cram,cram,930119400.0,6200796.0,SC RUN 22829 8#8,0:75 1:75,A:242979598;C:220045143;G:219448143;T:245941628;N:1704888,75,75,,,242979598,220045143,219448143,245941628,1704888,ERX3468737,ERS1806669,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95653,0.95946,0.14247,0.14149,0.6842,0.68738,0.4957,0.49737,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7939,ERR3446737,ERX3468736,ERS1806667,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 D2,SAMEA104147649,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147649|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:38729f20 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38729f20 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934952,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#7,DN488439N:G1,Illumina sequencing of library DN488439N:G1  constructed from sample accession ERS1806667 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence CAGATCTG.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#7.cram,cram,992301900.0,6615346.0,SC RUN 22829 8#7,0:75 1:75,A:259898582;C:233807624;G:233974368;T:262804375;N:1816951,75,75,,,259898582,233807624,233974368,262804375,1816951,ERX3468736,ERS1806667,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95492,0.95925,0.14,0.13935,0.68112,0.68312,0.50181,0.49932,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7940,ERR3446736,ERX3468735,ERS1806668,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 F2,SAMEA104147650,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147650|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:385e05b0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:385e05b0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934951,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#6,DN488439N:F1,Illumina sequencing of library DN488439N:F1  constructed from sample accession ERS1806668 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence GCCAATGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#6.cram,cram,875586600.0,5837244.0,SC RUN 22829 8#6,0:75 1:75,A:231423685;C:204253857;G:204201395;T:234093029;N:1614634,75,75,,,231423685,204253857,204201395,234093029,1614634,ERX3468735,ERS1806668,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95428,0.95811,0.15334,0.15296,0.67905,0.68256,0.50447,0.50735,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7941,ERR3446735,ERX3468734,ERS1806666,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 A4,SAMEA104147648,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147648|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:27Z|INSDC status:public|Submitter Id:384833c0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:384833c0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934950,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#5,DN488439N:E1,Illumina sequencing of library DN488439N:E1  constructed from sample accession ERS1806666 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence ACAGTGGT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#5.cram,cram,835599450.0,5570663.0,SC RUN 22829 8#5,0:75 1:75,A:221022844;C:194609457;G:194728372;T:223667754;N:1571023,75,75,,,221022844,194609457,194728372,223667754,1571023,ERX3468734,ERS1806666,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95389,0.95704,0.16434,0.16289,0.68363,0.68669,0.50299,0.51388,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7942,ERR3446734,ERX3468733,ERS1806664,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 F1,SAMEA104147646,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147646|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:3832aff0 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:3832aff0 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934949,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#4,DN488439N:D1,Illumina sequencing of library DN488439N:D1  constructed from sample accession ERS1806664 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TGACCACT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#4.cram,cram,891655350.0,5944369.0,SC RUN 22829 8#4,0:75 1:75,A:236505554;C:207018655;G:207193827;T:239299452;N:1637862,75,75,,,236505554,207018655,207193827,239299452,1637862,ERX3468733,ERS1806664,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95251,0.95547,0.16653,0.16502,0.68822,0.68984,0.51935,0.51421,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7943,ERR3446733,ERX3468732,ERS1806665,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 C2,SAMEA104147647,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147647|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:38138f30 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:38138f30 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934948,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#3,DN488439N:C1,Illumina sequencing of library DN488439N:C1  constructed from sample accession ERS1806665 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence TTAGGCAT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#3.cram,cram,888434250.0,5922895.0,SC RUN 22829 8#3,0:75 1:75,A:233268153;C:208683895;G:208766742;T:236094656;N:1620804,75,75,,,233268153,208683895,208766742,236094656,1620804,ERX3468732,ERS1806665,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95631,0.96066,0.14611,0.14537,0.68422,0.6854,0.50209,0.50377,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7944,ERR3446732,ERX3468731,ERS1806663,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 B3,SAMEA104147645,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147645|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:37fdbd40 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:37fdbd40 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934947,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#2,DN488439N:B1,Illumina sequencing of library DN488439N:B1  constructed from sample accession ERS1806663 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence CGATGTTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#2.cram,cram,883215600.0,5888104.0,SC RUN 22829 8#2,0:75 1:75,A:231296783;C:208055844;G:208135446;T:234080007;N:1647520,75,75,,,231296783,208055844,208135446,234080007,1647520,ERX3468731,ERS1806663,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95417,0.95779,0.14224,0.14158,0.67945,0.68178,0.49376,0.49496,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
7945,ERR3446731,ERX3468730,ERS1806662,ERP023267,PRJEB21045,RNASeq of zebrafish metabolic mutants,RNASeq_of_zebrafish_metabolic_mutants-sc-4765,Transcriptome Analysis,RNAseq data was generated from one or more alleles of zebrafish metabolic mutants for transcriptome analysis.,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2017 05 25|ArrayExpress:E ERAD 683,,,zmp ph279 E4,SAMEA104147644,Wellcome Sanger Institute,ArrayExpress DEVELOPMENTAL STAGE:Larval:Protruding mouth   ZFS:0000035|ArrayExpress ORGANISM PART:Whole organism|ArrayExpress SPECIES:Danio rerio|ArrayExpress STRAIN OR LINE:mixed|ENA first public:2019 06 29|ENA last update:2017 06 29|External Id:SAMEA104147644|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2019 06 29T04:02:25Z|INSDC last update:2017 06 29T14:54:26Z|INSDC status:public|Submitter Id:37e37e80 41ed 11e7 b6fe 3c4a9275d6c8|common name:zebrafish|sample name:37e37e80 41ed 11e7 b6fe 3c4a9275d6c8|subject id:4765STDY6934946,,,,,,,,,Illumina HiSeq 2500 paired end sequencing,SC EXP 22829 8#1,DN488439N:A1,Illumina sequencing of library DN488439N:A1  constructed from sample accession ERS1806662 for study accession ERP023267.  This is part of an Illumina multiplexed sequencing run 22829 8.  This submission includes reads tagged with the sequence ATCACGTT.,RNA seq dUTP eukaryotic,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP023267,Illumina HiSeq 2500 paired end sequencing,ENA FIRST PUBLIC:2019 07 22|ENA LAST UPDATE:2019 07 22,22829_8#1.cram,cram,832221450.0,5548143.0,SC RUN 22829 8#1,0:75 1:75,A:218233303;C:195802305;G:195652594;T:221003769;N:1529479,75,75,,,218233303,195802305,195652594,221003769,1529479,ERX3468730,ERS1806662,ERA2044656,European Nucleotide Archive,Wellcome Sanger Institute,2,0.95539,0.95958,0.13422,0.13299,0.68631,0.68828,0.49563,0.49505,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United Kingdom,2017-05-25,Larval,Larval,Whole Organism,All anatomical structures
9699,ERR3301006,ERX3327073,ERS3389661,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT embryo rep 3,SAMEA5585437,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585437|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 3|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 3 p,WT embryo rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_2.fq.gz,fastq fastq,7308473280.0,45677958.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo3 ,0:80 1:80,A:1898812783;C:1731426486;G:1757309247;T:1920031807;N:892957,80,80,,,1898812783,1731426486,1757309247,1920031807,892957,ERX3327073,ERS3389661,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94288,0.95671,0.07985,0.08023,0.67915,0.67815,0.47781,0.48461,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9700,ERR3301005,ERX3327072,ERS3389660,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT embryo rep 2,SAMEA5585436,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585436|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 2 p,WT embryo rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_2.fq.gz,fastq fastq,7424396000.0,46402475.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo2 ,0:80 1:80,A:1940921070;C:1754354124;G:1768688429;T:1959515088;N:917289,80,80,,,1940921070,1754354124,1768688429,1959515088,917289,ERX3327072,ERS3389660,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94222,0.95663,0.0909,0.09022,0.67929,0.67606,0.48763,0.48719,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9701,ERR3301004,ERX3327071,ERS3389659,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT embryo rep 1,SAMEA5585435,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585435|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 1 p,WT embryo rep  1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_2.fq.gz,fastq fastq,7300913760.0,45630711.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo1 ,0:80 1:80,A:1931507380;C:1703881934;G:1712942848;T:1951676424;N:905174,80,80,,,1931507380,1703881934,1712942848,1951676424,905174,ERX3327071,ERS3389659,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93831,0.95401,0.09471,0.09526,0.67576,0.67403,0.48092,0.48297,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9702,ERR3301003,ERX3327070,ERS3389658,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 3,SAMEA5585434,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585434|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:6|organism part:heart|sample name:E MTAB 7920:WT heart rep 3|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 3 p,WT heart rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz,fastq fastq,7339830080.0,45873938.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3 ,0:80 1:80,A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141,80,80,,,1985328994,1673818891,1695753386,1984031668,897141,ERX3327070,ERS3389658,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.9311,0.94858,0.07774,0.07789,0.76378,0.76394,0.52815,0.52065,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9703,ERR3301002,ERX3327069,ERS3389657,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 2,SAMEA5585433,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585433|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:5|organism part:heart|sample name:E MTAB 7920:WT heart rep 2|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 2 p,WT heart rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz,fastq fastq,7486415840.0,46790099.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2 ,0:80 1:80,A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493,80,80,,,2020798219,1702752807,1731176796,2030756525,931493,ERX3327069,ERS3389657,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93397,0.9509,0.07752,0.07859,0.76019,0.76002,0.54034,0.54728,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9704,ERR3301001,ERX3327068,ERS3389656,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 1,SAMEA5585432,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585432|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:4|organism part:heart|sample name:E MTAB 7920:WT heart rep 1|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 1 p,WT heart rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz,fastq fastq,6814600800.0,42591255.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1 ,0:80 1:80,A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985,80,80,,,1823108307,1567497576,1587567005,1835589927,837985,ERX3327068,ERS3389656,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93109,0.94806,0.07581,0.07635,0.75907,0.75988,0.54746,0.54753,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9705,ERR3301000,ERX3327067,ERS3389655,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant embryo rep 3,SAMEA5585431,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585431|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 3|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 3 p,Mutant embryo rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_2.fq.gz,fastq fastq,6323854560.0,39524091.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo3 ,0:80 1:80,A:1662088892;C:1473777430;G:1500364334;T:1686853051;N:770853,80,80,,,1662088892,1473777430,1500364334,1686853051,770853,ERX3327067,ERS3389655,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93548,0.95404,0.09034,0.09103,0.67584,0.67592,0.47892,0.48193,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9706,ERR3300999,ERX3327066,ERS3389654,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant embryo rep 2,SAMEA5585430,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585430|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 2|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 2 p,Mutant embryo rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_2.fq.gz,fastq fastq,6564227680.0,41026423.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo2 ,0:80 1:80,A:1702331829;C:1557343680;G:1583770440;T:1719974488;N:807243,80,80,,,1702331829,1557343680,1583770440,1719974488,807243,ERX3327066,ERS3389654,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94141,0.95836,0.07518,0.07501,0.67982,0.67803,0.47895,0.47763,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9707,ERR3300998,ERX3327065,ERS3389653,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant embryo rep 1,SAMEA5585429,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585429|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 1|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 1 p,Mutant embryo rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_2.fq.gz,fastq fastq,6991429280.0,43696433.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo1 ,0:80 1:80,A:1852543850;C:1630880197;G:1635963943;T:1871173669;N:867621,80,80,,,1852543850,1630880197,1635963943,1871173669,867621,ERX3327065,ERS3389653,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93819,0.95201,0.10106,0.10107,0.67541,0.67523,0.4792,0.48253,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9708,ERR3300997,ERX3327064,ERS3389652,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 3,SAMEA5585428,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585428|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:3|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 3|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 3 p,Mutant heart rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz,fastq fastq,7240447520.0,45252797.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3 ,0:80 1:80,A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957,80,80,,,1968283412,1645458614,1652590010,1973242527,872957,ERX3327064,ERS3389652,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.92784,0.94597,0.08601,0.08686,0.76702,0.76449,0.50929,0.52685,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9709,ERR3300996,ERX3327063,ERS3389651,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 2,SAMEA5585427,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585427|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:2|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 2|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 2 p,Mutant heart rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz,fastq fastq,7347029600.0,45918935.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2 ,0:80 1:80,A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229,80,80,,,1967915665,1690507331,1712776156,1974918219,912229,ERX3327063,ERS3389651,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93337,0.94978,0.07673,0.07724,0.76755,0.76798,0.53415,0.51157,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9710,ERR3300995,ERX3327062,ERS3389650,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 1,SAMEA5585426,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:02Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585426|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:02Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:1|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 1|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 1 p,Mutant heart rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz,fastq fastq,6296502880.0,39353143.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1 ,0:80 1:80,A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941,80,80,,,1677737687,1460767489,1468915029,1688319734,762941,ERX3327062,ERS3389650,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93775,0.9516,0.07994,0.08077,0.75844,0.75759,0.51937,0.52207,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9816,ERR3957806,ERX3965610,ERS4355893,ERP120207,PRJEB36940,RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,E-MTAB-8824,Transcriptome Analysis,Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose  redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4  FBLN5  LTBP4 and ELN  encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1  ATP6V1A  ATP6V0A2  ALDH18A1  RIN2  GORAB  PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds  variable mental disability  typical facial characteristics  lipodystrophy  hypotonia  and cardiopulmonary involvement including pneumothorax  hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up  or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis  we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b  disrupting transcription atp6v1e1bhi577aTg/+  from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b  c.334insGG; c.337 340delCGG  predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis.   Overview of the experimental work flow:   Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later   RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions   RNA integrity: 2100 Bioanalyzer Agilent   Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina   Sequencing: HiSeq 3000 sequencer Illumina   paired end 150 bp   sequencing facility of the Center of Medical Genetics Ghent   alignement to zebrafish GRCz10 reference genome to generate bam files    RNA seq pipeline was used that was published by the nf core community. This pipeline was executed using the Nextflow engine for computational workflows and comprises several processing steps. QC analysis of the RNA seq data was performed with FastQC and MultiQC. TrimGalore was used to remove adapter contamination and to trim low quality regions. Duplicate reads were identified with MarkDuplicates. Subsequently  all cleaned and trimmed reads that passed QC were aligned to GRCz10 using STAR aligner. Gene counts were computed using the featureCounts package. Differential expression analysis subsequently was performed on these gene counts using DESeq2. Differentially expressed genes were identified using a fold change cut off >1 and FDR=0.05. Finally  GO enrichment & pathway analysis were performed on differentially expressed gene sets using the Generally Applicable Gene set Enrichment for Pathway Analysis GAGE algorithm.,ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26,,Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina.,atp6v1e1b hi577aTg/hi577aTg 3,SAMEA6591599,"Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University",ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591599|INSDC center name:Center for Medical Genetics Ghent  Ghent University Hospital  Ghent  Belgium Department of biomolecular medicine  Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:insertion|genotype:atp6v1e1b hi577aTg/hi577aTg|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3|scientific name:Danio rerio|sex:male|strain:AB,,,,,,,,,Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 3 p,atp6v1e1b hi577aTg/hi577aTg 3 p,RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina.,Experimental Factor: genotype:atp6v1e1b hi577aTg/hi577aTg|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP120207,Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26,atp6v1e1b_hi577aTghi577aTg_3_R1.fastq.gz atp6v1e1b_hi577aTghi577aTg_3_R2.fastq.gz,fastq fastq,9237478586.0,31595868.0,E MTAB 8824:atp6v1e1b hi577aTghi577aTg 3 R,0:146.21 1:146.15,A:2400784505;C:2208559586;G:2203025457;T:2422549514;N:2559524,146,146,,,2400784505,2208559586,2203025457,2422549514,2559524,ERX3965610,ERS4355893,ERA2393549,"Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive","Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive",2,0.95009,0.95029,0.06098,0.05862,0.66736,0.67614,0.46036,0.46726,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2020-02-26,Larval,Larval,Whole Organism,All anatomical structures
9817,ERR3957805,ERX3965609,ERS4355892,ERP120207,PRJEB36940,RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,E-MTAB-8824,Transcriptome Analysis,Cutis laxa CL syndromes are a heterogenous group of connective tissue disorders that share a loose  redundant skin as a common clinical feature. The systemic features vary among the different subtypes. CL is caused by mutations in genes encoding for components of the extracellular matrix FBLN4  FBLN5  LTBP4 and ELN  encoding for elastin modifying enzymes ATP7A or encoding for components that influence cellular trafficking and metabolism ATP6V1E1  ATP6V1A  ATP6V0A2  ALDH18A1  RIN2  GORAB  PYCR1 and SLC2A10. ATP6V1E1–related CL cause loose redundant skin folds  variable mental disability  typical facial characteristics  lipodystrophy  hypotonia  and cardiopulmonary involvement including pneumothorax  hypertrophic cardiomyopathy and aortic root dilatation. The intent of this study is to investigate which genes are up  or downregulated in atp6v1e1b deficient zebrafish larvae compared to wild type controls. Via transcriptome analysis  we want to study the pathogenic mechanism of ATP6V1E1 induced CL syndrome. We use a zebrafish line with viral insertion in the five primeUTR of atp6v1e1b  disrupting transcription atp6v1e1bhi577aTg/+  from the Zebrafish International Research Center ZIRC and we use a line harboring a two base pair insertion followed by a three base pair deletion in exon 5 of atp6v1e1b  c.334insGG; c.337 340delCGG  predicted to result in p.R111WfsX2 atp6v1e1bcmg78/+ which we created ourselves by CRISPR Cas9 mutagenesis.   Overview of the experimental work flow:   Sample collection: pool of 10 zebrafish larvae of 3 dpf/genotype in RNA later   RNA extraction: TRIzol® Reagent RNeasy mini kit Qiagen according to manufacturer's instructions   RNA integrity: 2100 Bioanalyzer Agilent   Sequencing library: TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina   Sequencing: HiSeq 3000 sequencer Illumina   paired end 150 bp   sequencing facility of the Center of Medical Genetics Ghent   alignement to zebrafish GRCz10 reference genome to generate bam files    RNA seq pipeline was used that was published by the nf core community. This pipeline was executed using the Nextflow engine for computational workflows and comprises several processing steps. QC analysis of the RNA seq data was performed with FastQC and MultiQC. TrimGalore was used to remove adapter contamination and to trim low quality regions. Duplicate reads were identified with MarkDuplicates. Subsequently  all cleaned and trimmed reads that passed QC were aligned to GRCz10 using STAR aligner. Gene counts were computed using the featureCounts package. Differential expression analysis subsequently was performed on these gene counts using DESeq2. Differentially expressed genes were identified using a fold change cut off >1 and FDR=0.05. Finally  GO enrichment & pathway analysis were performed on differentially expressed gene sets using the Generally Applicable Gene set Enrichment for Pathway Analysis GAGE algorithm.,ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26,,Protocols: Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina.,atp6v1e1b hi577aTg/hi577aTg 2,SAMEA6591598,"Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University",ENA FIRST PUBLIC:2020 08 03T04:04:15Z|ENA LAST UPDATE:2020 02 26T13:29:54Z|External Id:SAMEA6591598|INSDC center name:Center for Medical Genetics Ghent  Ghent University Hospital  Ghent  Belgium Department of biomolecular medicine  Ghent University|INSDC first public:2020 08 03T04:04:15Z|INSDC last update:2020 02 26T13:29:54Z|INSDC status:public|Submitter Id:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|disease:Autosomal recessive cutis laxa type 2A|disease staging:before the gross morphological phenotype becomes apparent|genetic modification:insertion|genotype:atp6v1e1b hi577aTg/hi577aTg|individual:pool of 10 larvae|organism part:whole organism|phenotype:atp6v1e1b deletion|replicate:biological replicate|sample name:E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2|scientific name:Danio rerio|sex:male|strain:AB,,,,,,,,,Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,E MTAB 8824:atp6v1e1b hi577aTg/hi577aTg 2 p,atp6v1e1b hi577aTg/hi577aTg 2 p,RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,Whole zebrafish larvae at 3 dpf were genotyped before collection in RNA later. Total RNA was isolated from whole zebrafish larvae at 3 dpf from atp6v1e1bcmg78zebrafish and atp6v1e1bhi577aTg zebrafish together with their respective controls using TRIzol® Reagent followed by a purification with the RNeasy mini kit Qiagen according to manufacturer's instructions. RNA integrity was checked by 2100 Bioanalyzer Agilent. 10 zebrafish larvae of each genotype were pooled in 1 sample to obtain sufficient heterogeneity amongst samples Sequencing library was prepared according to the manufacturer's instructions of the TruSeq® Stranded mRNA Library Prep Illumina  San Diego  California  United States supplemented with TruSeq® RNA Single Indexes Set A Illumina.,Experimental Factor: genotype:atp6v1e1b hi577aTg/hi577aTg|Experimental Factor: disease:Autosomal recessive cutis laxa type 2A,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,ERP120207,Illumina HiSeq 3000 paired end sequencing; RNA seq of whole tissue of 3 dpf atp6v1e1b deficient zebrafish larvae and wild type controls,ENA FIRST PUBLIC:2021 01 29|ENA LAST UPDATE:2020 02 26,atp6v1e1b_hi577aTghi577aTg_2_R1.fastq.gz atp6v1e1b_hi577aTghi577aTg_2_R2.fastq.gz,fastq fastq,12062097051.0,41147017.0,E MTAB 8824:atp6v1e1b hi577aTghi577aTg 2 R,0:146.61 1:146.54,A:3154735338;C:2867420665;G:2850251799;T:3187999165;N:1690084,146,146,,,3154735338,2867420665,2850251799,3187999165,1690084,ERX3965609,ERS4355892,ERA2393549,"Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive","Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium Department of biomolecular medicine, Ghent University|European Nucleotide Archive",2,0.94863,0.94866,0.0678,0.06563,0.66421,0.67188,0.46715,0.45279,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Belgium,2020-02-26,Larval,Larval,Whole Organism,All anatomical structures