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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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 6000,1510Application ReadForward11Application ReadReverse76,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
175,DRR084197,DRX078028,DRS086522,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2],SAMD00073604,,sample name:M 4th|replicate:biological replicate 2,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073604,DRX078028,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,360Application ReadForward1,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073604,,,,1389837888.0,38606608.0,DRR084197,0:36,A:320671418;C:336948866;G:347550258;T:381720581;N:2946765,36,,,,320671418,336948866,347550258,381720581,2946765,DRX078028,DRS086522,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.89763,,0.02235,,0.76445,,0.46381,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
181,DRR084191,DRX078022,DRS086516,DRP004758,PRJDB5490,Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish,DRP004758,Other,Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.,,,natural paring early sample,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1],SAMD00073598,,sample name:M|replicate:biological replicate 1,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00073598,DRX078022,zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1],1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,360Application ReadForward1,DRP004758,Illumina HiSeq 2500 sequencing of SAMD00073598,,,,1050981012.0,29193917.0,DRR084191,0:36,A:241048832;C:256186268;G:260277071;T:293299597;N:169244,36,,,,241048832,256186268,260277071,293299597,169244,DRX078022,DRS086516,DRA005484,SHIZUOKA|Shizuoka University,Shizuoka University,1,0.9088,,0.02369,,0.7624,,0.47998,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-01-23,Zygote,Embryo,Multi-tissue,Multi-system
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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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 6000,2000Application ReadForward11Application ReadReverse101,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
9898,ERR4194114,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 2,SAMEA6873729,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 2 s,Sample 2 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:8|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA8h_1_S2_L001.bam,bam,10087287534.0,99874134.0,E MTAB 9193:cDNA8h 1 S2 L001,0:101,A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403,101,,,,2892833391,2022466595,2198646699,2962268446,11072403,ERX4155254,ERS4601292,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93609,,0.12902,,0.82158,,0.5062,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9899,ERR4194115,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 2,SAMEA6873729,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 2 s,Sample 2 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:8|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA8h_1_S2_L002.bam,bam,10191911414.0,100910014.0,E MTAB 9193:cDNA8h 1 S2 L002,0:101,A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577,101,,,,2923216190,2043975715,2221734566,2992798366,10186577,ERX4155254,ERS4601292,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93445,,0.13038,,0.824,,0.49774,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9900,ERR4194112,ERX4155253,ERS4601291,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 1,SAMEA6873728,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 1 s,Sample 1 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:6|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA6h_1_S1_L001.bam,bam,7181772357.0,71106657.0,E MTAB 9193:cDNA6h 1 S1 L001,0:101,A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877,101,,,,2074032710,1415439071,1544274166,2140112533,7913877,ERX4155253,ERS4601291,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.9297,,0.12156,,0.8117,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9901,ERR4194113,ERX4155253,ERS4601291,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 1,SAMEA6873728,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 1 s,Sample 1 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:6|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA6h_1_S1_L002.bam,bam,7256542253.0,71846953.0,E MTAB 9193:cDNA6h 1 S1 L002,0:101,A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509,101,,,,2096163385,1430325700,1560530043,2162265616,7257509,ERX4155253,ERS4601291,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.92882,,0.12127,,0.81162,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9902,ERR4194128,ERX4155256,ERS4601294,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 4,SAMEA6873731,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 4 s,Sample 4 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_1_control_S1_L001.bam,bam,10785974123.0,106791823.0,E MTAB 9193:cDNA13h 1 control S1 L001,0:101,A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809,101,,,,3007305661,2241057062,2505494392,2986021199,46095809,ERX4155256,ERS4601294,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.67094,,0.07571,,0.92951,,0.5272,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9903,ERR4194129,ERX4155256,ERS4601294,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 4,SAMEA6873731,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 4 s,Sample 4 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_1_control_S1_L002.bam,bam,10595192294.0,104902894.0,E MTAB 9193:cDNA13h 1 control S1 L002,0:101,A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823,101,,,,2971916419,2204229263,2390854035,2949877754,78314823,ERX4155256,ERS4601294,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.67255,,0.08054,,0.91583,,0.52661,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9904,ERR4194116,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L001.bam,bam,1622536412.0,16556494.0,E MTAB 9193:cDNA10h 1 S3 L001,0:98,A:491141175;C:317161060;G:354179755;T:459976409;N:78013,98,,,,491141175,317161060,354179755,459976409,78013,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93238,,0.13033,,0.89132,,0.47076,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9905,ERR4194117,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L002.bam,bam,1484328776.0,15146212.0,E MTAB 9193:cDNA10h 1 S3 L002,0:98,A:450782055;C:290088574;G:322801188;T:420570801;N:86158,98,,,,450782055,290088574,322801188,420570801,86158,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.92846,,0.13128,,0.89923,,0.46879,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9906,ERR4194118,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L003.bam,bam,1578833116.0,16110542.0,E MTAB 9193:cDNA10h 1 S3 L003,0:98,A:477600666;C:308260969;G:347303289;T:445467384;N:200808,98,,,,477600666,308260969,347303289,445467384,200808,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93107,,0.12965,,0.91265,,0.47375,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9907,ERR4194119,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L004.bam,bam,1859564994.0,18975153.0,E MTAB 9193:cDNA10h 1 S3 L004,0:98,A:562936790;C:364057256;G:406607636;T:525811595;N:151717,98,,,,562936790,364057256,406607636,525811595,151717,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93453,,0.1266,,0.87714,,0.46957,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9908,ERR4194120,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L001.bam,bam,1156341102.0,11799399.0,E MTAB 9193:cDNA10h 2 S3 L001,0:98,A:345857612;C:224453195;G:257551986;T:327969064;N:509245,98,,,,345857612,224453195,257551986,327969064,509245,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93863,,0.10744,,0.81984,,0.501,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9909,ERR4194121,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L002.bam,bam,1105219696.0,11277752.0,E MTAB 9193:cDNA10h 2 S3 L002,0:98,A:331051973;C:214369903;G:246546338;T:312897773;N:353709,98,,,,331051973,214369903,246546338,312897773,353709,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93941,,0.10818,,0.82211,,0.50079,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9910,ERR4194122,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L003.bam,bam,1105199606.0,11277547.0,E MTAB 9193:cDNA10h 2 S3 L003,0:98,A:331158619;C:214305131;G:246465559;T:312930408;N:339889,98,,,,331158619,214305131,246465559,312930408,339889,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93767,,0.10645,,0.82329,,0.50057,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9911,ERR4194123,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L004.bam,bam,1108707712.0,11313344.0,E MTAB 9193:cDNA10h 2 S3 L004,0:98,A:331374433;C:215925150;G:247131942;T:313865174;N:411013,98,,,,331374433,215925150,247131942,313865174,411013,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93827,,0.10842,,0.82031,,0.49241,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9912,ERR4194124,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L005.bam,bam,1110084612.0,11327394.0,E MTAB 9193:cDNA10h 2 S3 L005,0:98,A:332881960;C:215360330;G:247563319;T:313842331;N:436672,98,,,,332881960,215360330,247563319,313842331,436672,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93827,,0.10719,,0.8238,,0.50406,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9913,ERR4194125,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L006.bam,bam,1113812728.0,11365436.0,E MTAB 9193:cDNA10h 2 S3 L006,0:98,A:333112288;C:216649152;G:248341020;T:315338848;N:371420,98,,,,333112288,216649152,248341020,315338848,371420,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93843,,0.10675,,0.82079,,0.49284,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9914,ERR4194126,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L007.bam,bam,1119495748.0,11423426.0,E MTAB 9193:cDNA10h 2 S3 L007,0:98,A:335288339;C:217283719;G:249624836;T:316900388;N:398466,98,,,,335288339,217283719,249624836,316900388,398466,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93711,,0.10749,,0.82266,,0.49382,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9915,ERR4194127,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L008.bam,bam,1175946688.0,11999456.0,E MTAB 9193:cDNA10h 2 S3 L008,0:98,A:351364169;C:228318193;G:261971072;T:333863943;N:429311,98,,,,351364169,228318193,261971072,333863943,429311,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93851,,0.10755,,0.82158,,0.49895,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9916,ERR4194130,ERX4155257,ERS4601295,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 5,SAMEA6873732,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 5 s,Sample 5 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_2_gata56KD_S2_L001.bam,bam,7791309377.0,77141677.0,E MTAB 9193:cDNA13h 2 gata56KD S2 L001,0:101,A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267,101,,,,2198242220,1593746618,1784167452,2181979820,33173267,ERX4155257,ERS4601295,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.66736,,0.08039,,0.93026,,0.50796,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9917,ERR4194131,ERX4155257,ERS4601295,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6 8 10 13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 5,SAMEA6873732,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology Sickkids Toronto Canada; Genetics and Genome Biology Sickkids Toronto Canada; Molecular Genetics University of Toronto Toronto Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 5 s,Sample 5 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf 8 hpf 10 hpf the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl 2.6 mM KCl 5 mM HEPE pH 7.0 for 5 min followed by 500ul TrpLE GIBCO TrypLE Express Enzyme cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO Trypsin2.5% no phenol red cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_2_gata56KD_S2_L002.bam,bam,7658149967.0,75823267.0,E MTAB 9193:cDNA13h 2 gata56KD S2 L002,0:101,A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859,101,,,,2172230233,1568805100,1703587704,2157181071,56345859,ERX4155257,ERS4601295,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.66565,,0.08597,,0.91804,,0.51772,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
10008,ERR4648708,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L001_R1_001.fastq.gz 15S6_S11_L001_R2_001.fastq.gz,fastq fastq,1591537736.0,10470643.0,E MTAB 9615:15S6 S11 L001 R,0:76 1:76,A:429238832;C:363616036;G:370142973;T:428278902;N:260993,76,76,,,429238832,363616036,370142973,428278902,260993,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94838,0.95275,0.11825,0.11227,0.67263,0.67535,0.47339,0.48683,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10009,ERR4648709,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L002_R1_001.fastq.gz 15S6_S11_L002_R2_001.fastq.gz,fastq fastq,1559456464.0,10259582.0,E MTAB 9615:15S6 S11 L002 R,0:76 1:76,A:420535603;C:356234776;G:362907355;T:419528118;N:250612,76,76,,,420535603,356234776,362907355,419528118,250612,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94922,0.95244,0.11903,0.11395,0.66931,0.67233,0.46849,0.48097,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10010,ERR4648710,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L003_R1_001.fastq.gz 15S6_S11_L003_R2_001.fastq.gz,fastq fastq,1611815600.0,10604050.0,E MTAB 9615:15S6 S11 L003 R,0:76 1:76,A:434815382;C:368453005;G:374802612;T:433582623;N:161978,76,76,,,434815382,368453005,374802612,433582623,161978,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94878,0.9521,0.11889,0.11284,0.67302,0.67521,0.47879,0.48281,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10011,ERR4648711,ERX4572379,ERS5128759,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S6,SAMEA7370309,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370309|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S6 p,15S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S6_S11_L004_R1_001.fastq.gz 15S6_S11_L004_R2_001.fastq.gz,fastq fastq,1587249512.0,10442431.0,E MTAB 9615:15S6 S11 L004 R,0:76 1:76,A:428113406;C:362725542;G:369262476;T:427024700;N:123388,76,76,,,428113406,362725542,369262476,427024700,123388,ERX4572379,ERS5128759,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94868,0.95237,0.11954,0.1137,0.66888,0.67411,0.48327,0.48573,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10012,ERR4648704,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L001_R1_001.fastq.gz 15S5_S7_L001_R2_001.fastq.gz,fastq fastq,1695774928.0,11156414.0,E MTAB 9615:15S5 S7 L001 R,0:76 1:76,A:456096603;C:390987096;G:394091205;T:454321430;N:278594,76,76,,,456096603,390987096,394091205,454321430,278594,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94681,0.9507,0.14362,0.13726,0.67931,0.68087,0.49708,0.49164,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10013,ERR4648705,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L002_R1_001.fastq.gz 15S5_S7_L002_R2_001.fastq.gz,fastq fastq,1652445504.0,10871352.0,E MTAB 9615:15S5 S7 L002 R,0:76 1:76,A:444752710;C:381030057;G:383777650;T:442619007;N:266080,76,76,,,444752710,381030057,383777650,442619007,266080,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94649,0.94993,0.14201,0.1357,0.68124,0.68471,0.49354,0.48934,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10014,ERR4648706,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L003_R1_001.fastq.gz 15S5_S7_L003_R2_001.fastq.gz,fastq fastq,1721026536.0,11322543.0,E MTAB 9615:15S5 S7 L003 R,0:76 1:76,A:463210590;C:396958291;G:399739948;T:460942070;N:175637,76,76,,,463210590,396958291,399739948,460942070,175637,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94689,0.95134,0.14445,0.13799,0.68083,0.68308,0.4907,0.49184,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10015,ERR4648707,ERX4572378,ERS5128758,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S5,SAMEA7370308,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370308|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S5 p,15S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S5_S7_L004_R1_001.fastq.gz 15S5_S7_L004_R2_001.fastq.gz,fastq fastq,1681600624.0,11063162.0,E MTAB 9615:15S5 S7 L004 R,0:76 1:76,A:452919887;C:387692803;G:390415798;T:450439351;N:132785,76,76,,,452919887,387692803,390415798,450439351,132785,ERX4572378,ERS5128758,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94692,0.95086,0.14315,0.13615,0.67992,0.68272,0.49657,0.49082,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10016,ERR4648700,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L001_R1_001.fastq.gz 15S1_S3_L001_R2_001.fastq.gz,fastq fastq,1684976544.0,11085372.0,E MTAB 9615:15S1 S3 L001 R,0:76 1:76,A:459213104;C:380435364;G:388061620;T:456986886;N:279570,76,76,,,459213104,380435364,388061620,456986886,279570,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94815,0.95291,0.11703,0.10838,0.69106,0.69256,0.48318,0.48685,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10017,ERR4648701,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L002_R1_001.fastq.gz 15S1_S3_L002_R2_001.fastq.gz,fastq fastq,1643737728.0,10814064.0,E MTAB 9615:15S1 S3 L002 R,0:76 1:76,A:448110182;C:371404635;G:378168271;T:445793393;N:261247,76,76,,,448110182,371404635,378168271,445793393,261247,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94922,0.95393,0.11448,0.10652,0.69134,0.69301,0.4816,0.48594,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10018,ERR4648702,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L003_R1_001.fastq.gz 15S1_S3_L003_R2_001.fastq.gz,fastq fastq,1703808888.0,11209269.0,E MTAB 9615:15S1 S3 L003 R,0:76 1:76,A:464594650;C:384747658;G:392231421;T:462069215;N:165944,76,76,,,464594650,384747658,392231421,462069215,165944,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94969,0.95388,0.11731,0.10782,0.6914,0.69325,0.48074,0.48209,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10019,ERR4648703,ERX4572377,ERS5128757,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15S1,SAMEA7370307,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370307|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15S1 p,15S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15S1_S3_L004_R1_001.fastq.gz 15S1_S3_L004_R2_001.fastq.gz,fastq fastq,1668108648.0,10974399.0,E MTAB 9615:15S1 S3 L004 R,0:76 1:76,A:455048996;C:376727183;G:383710020;T:452489191;N:133258,76,76,,,455048996,376727183,383710020,452489191,133258,ERX4572377,ERS5128757,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94927,0.95254,0.11691,0.10738,0.68956,0.69244,0.48172,0.48334,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10020,ERR4648696,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L001_R1_001.fastq.gz 15K6_S12_L001_R2_001.fastq.gz,fastq fastq,1609873040.0,10591270.0,E MTAB 9615:15K6 S12 L001 R,0:76 1:76,A:437147858;C:366192064;G:371108418;T:435155810;N:268890,76,76,,,437147858,366192064,371108418,435155810,268890,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94722,0.95179,0.13705,0.12981,0.67679,0.67866,0.48396,0.49346,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10021,ERR4648697,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L002_R1_001.fastq.gz 15K6_S12_L002_R2_001.fastq.gz,fastq fastq,1575514808.0,10365229.0,E MTAB 9615:15K6 S12 L002 R,0:76 1:76,A:428185491;C:358401918;G:362831429;T:425840762;N:255208,76,76,,,428185491,358401918,362831429,425840762,255208,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94785,0.9528,0.13846,0.13087,0.67592,0.67856,0.49265,0.48858,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10022,ERR4648698,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L003_R1_001.fastq.gz 15K6_S12_L003_R2_001.fastq.gz,fastq fastq,1630087216.0,10724258.0,E MTAB 9615:15K6 S12 L003 R,0:76 1:76,A:442997697;C:370859421;G:375516402;T:440546052;N:167644,76,76,,,442997697,370859421,375516402,440546052,167644,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94716,0.95256,0.13708,0.12903,0.67608,0.6804,0.48953,0.49399,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10023,ERR4648699,ERX4572376,ERS5128756,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K6,SAMEA7370306,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370306|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K6 p,15K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K6_S12_L004_R1_001.fastq.gz 15K6_S12_L004_R2_001.fastq.gz,fastq fastq,1598521832.0,10516591.0,E MTAB 9615:15K6 S12 L004 R,0:76 1:76,A:434619516;C:363630314;G:368039060;T:432106642;N:126300,76,76,,,434619516,363630314,368039060,432106642,126300,ERX4572376,ERS5128756,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9476,0.95293,0.1363,0.12951,0.67677,0.67831,0.4896,0.48586,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10024,ERR4648692,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L001_R1_001.fastq.gz 15K5_S8_L001_R2_001.fastq.gz,fastq fastq,1615900448.0,10630924.0,E MTAB 9615:15K5 S8 L001 R,0:76 1:76,A:434660709;C:371711237;G:375977073;T:433284563;N:266866,76,76,,,434660709,371711237,375977073,433284563,266866,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94975,0.95448,0.13643,0.13022,0.68243,0.68266,0.48919,0.49247,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10025,ERR4648693,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L002_R1_001.fastq.gz 15K5_S8_L002_R2_001.fastq.gz,fastq fastq,1578139392.0,10382496.0,E MTAB 9615:15K5 S8 L002 R,0:76 1:76,A:424647045;C:363127751;G:366920105;T:423189068;N:255423,76,76,,,424647045,363127751,366920105,423189068,255423,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94906,0.95028,0.13531,0.12984,0.68045,0.68237,0.48576,0.48791,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10026,ERR4648694,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L003_R1_001.fastq.gz 15K5_S8_L003_R2_001.fastq.gz,fastq fastq,1639204480.0,10784240.0,E MTAB 9615:15K5 S8 L003 R,0:76 1:76,A:441158676;C:377209170;G:381225501;T:439441707;N:169426,76,76,,,441158676,377209170,381225501,439441707,169426,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94969,0.95069,0.13506,0.12904,0.68045,0.68318,0.48642,0.48116,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10027,ERR4648695,ERX4572375,ERS5128755,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K5,SAMEA7370305,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370305|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K5 p,15K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K5_S8_L004_R1_001.fastq.gz 15K5_S8_L004_R2_001.fastq.gz,fastq fastq,1605273824.0,10561012.0,E MTAB 9615:15K5 S8 L004 R,0:76 1:76,A:432120953;C:369415812;G:373183577;T:430423263;N:130219,76,76,,,432120953,369415812,373183577,430423263,130219,ERX4572375,ERS5128755,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95,0.95371,0.13552,0.12855,0.68225,0.68501,0.48758,0.48873,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10028,ERR4648688,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L001_R1_001.fastq.gz 15K1_S4_L001_R2_001.fastq.gz,fastq fastq,1723024576.0,11335688.0,E MTAB 9615:15K1 S4 L001 R,0:76 1:76,A:478023461;C:380533603;G:386774939;T:477400237;N:292336,76,76,,,478023461,380533603,386774939,477400237,292336,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94662,0.95081,0.13443,0.12127,0.68582,0.68895,0.48495,0.48494,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10029,ERR4648689,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L002_R1_001.fastq.gz 15K1_S4_L002_R2_001.fastq.gz,fastq fastq,1671563912.0,10997131.0,E MTAB 9615:15K1 S4 L002 R,0:76 1:76,A:463642862;C:369576882;G:375034721;T:463043696;N:265751,76,76,,,463642862,369576882,375034721,463043696,265751,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94621,0.95036,0.1321,0.12108,0.68408,0.68838,0.49122,0.47456,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10030,ERR4648690,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L003_R1_001.fastq.gz 15K1_S4_L003_R2_001.fastq.gz,fastq fastq,1750906392.0,11519121.0,E MTAB 9615:15K1 S4 L003 R,0:76 1:76,A:486163392;C:386732615;G:392751931;T:485086491;N:171963,76,76,,,486163392,386732615,392751931,485086491,171963,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94645,0.95048,0.1337,0.12075,0.68515,0.68895,0.48772,0.48793,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10031,ERR4648691,ERX4572374,ERS5128754,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,15K1,SAMEA7370304,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370304|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:15K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm15] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:15K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:15K1 p,15K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm15] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,15K1_S4_L004_R1_001.fastq.gz 15K1_S4_L004_R2_001.fastq.gz,fastq fastq,1706814232.0,11229041.0,E MTAB 9615:15K1 S4 L004 R,0:76 1:76,A:473795394;C:377133120;G:382846006;T:472903226;N:136486,76,76,,,473795394,377133120,382846006,472903226,136486,ERX4572374,ERS5128754,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94725,0.94973,0.13327,0.12016,0.68562,0.68954,0.49105,0.49467,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10032,ERR4648684,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L001_R1_001.fastq.gz 13S6_S9_L001_R2_001.fastq.gz,fastq fastq,1841379680.0,12114340.0,E MTAB 9615:13S6 S9 L001 R,0:76 1:76,A:497786486;C:421002484;G:426037843;T:496245838;N:307029,76,76,,,497786486,421002484,426037843,496245838,307029,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94902,0.95197,0.13858,0.13068,0.67578,0.67821,0.49162,0.5001,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10033,ERR4648685,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L002_R1_001.fastq.gz 13S6_S9_L002_R2_001.fastq.gz,fastq fastq,1800489248.0,11845324.0,E MTAB 9615:13S6 S9 L002 R,0:76 1:76,A:487141754;C:411696441;G:416253811;T:485107559;N:289683,76,76,,,487141754,411696441,416253811,485107559,289683,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94877,0.95202,0.13877,0.13209,0.67219,0.67554,0.49283,0.4882,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10034,ERR4648686,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L003_R1_001.fastq.gz 13S6_S9_L003_R2_001.fastq.gz,fastq fastq,1865349776.0,12272038.0,E MTAB 9615:13S6 S9 L003 R,0:76 1:76,A:504623109;C:426658328;G:431280260;T:502598105;N:189974,76,76,,,504623109,426658328,431280260,502598105,189974,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9488,0.95158,0.1382,0.1322,0.67326,0.67823,0.48581,0.49211,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10035,ERR4648687,ERX4572373,ERS5128753,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S6,SAMEA7370303,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370303|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S6 p,13S6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S6_S9_L004_R1_001.fastq.gz 13S6_S9_L004_R2_001.fastq.gz,fastq fastq,1829433392.0,12035746.0,E MTAB 9615:13S6 S9 L004 R,0:76 1:76,A:495172080;C:418346805;G:422823193;T:492947631;N:143683,76,76,,,495172080,418346805,422823193,492947631,143683,ERX4572373,ERS5128753,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94838,0.95203,0.13783,0.13154,0.67347,0.67702,0.49097,0.48982,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10036,ERR4648680,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L001_R1_001.fastq.gz 13S5_S5_L001_R2_001.fastq.gz,fastq fastq,1764129328.0,11606114.0,E MTAB 9615:13S5 S5 L001 R,0:76 1:76,A:481605171;C:399386009;G:402681794;T:480152811;N:303543,76,76,,,481605171,399386009,402681794,480152811,303543,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94669,0.95053,0.12759,0.12265,0.6758,0.67787,0.48204,0.48571,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10037,ERR4648681,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L002_R1_001.fastq.gz 13S5_S5_L002_R2_001.fastq.gz,fastq fastq,1720255136.0,11317468.0,E MTAB 9615:13S5 S5 L002 R,0:76 1:76,A:469777402;C:389359060;G:392798842;T:468039297;N:280535,76,76,,,469777402,389359060,392798842,468039297,280535,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94584,0.94469,0.12714,0.1201,0.67556,0.67787,0.46946,0.48243,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10038,ERR4648682,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L003_R1_001.fastq.gz 13S5_S5_L003_R2_001.fastq.gz,fastq fastq,1782008784.0,11723742.0,E MTAB 9615:13S5 S5 L003 R,0:76 1:76,A:486839858;C:403504903;G:406596413;T:484891715;N:175895,76,76,,,486839858,403504903,406596413,484891715,175895,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94547,0.94921,0.1273,0.12142,0.67487,0.67724,0.48324,0.48226,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10039,ERR4648683,ERX4572372,ERS5128752,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S5,SAMEA7370302,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370302|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S5 p,13S5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S5_S5_L004_R1_001.fastq.gz 13S5_S5_L004_R2_001.fastq.gz,fastq fastq,1745683368.0,11484759.0,E MTAB 9615:13S5 S5 L004 R,0:76 1:76,A:476931443;C:395203177;G:398442382;T:474964685;N:141681,76,76,,,476931443,395203177,398442382,474964685,141681,ERX4572372,ERS5128752,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94627,0.94906,0.12677,0.12035,0.67551,0.67763,0.47924,0.4843,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10040,ERR4648676,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L001_R1_001.fastq.gz 13S1_S1_L001_R2_001.fastq.gz,fastq fastq,1675492352.0,11022976.0,E MTAB 9615:13S1 S1 L001 R,0:76 1:76,A:455402707;C:380201647;G:385200827;T:454410247;N:276924,76,76,,,455402707,380201647,385200827,454410247,276924,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94815,0.94794,0.12103,0.1129,0.69327,0.69652,0.48471,0.48643,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10041,ERR4648677,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L002_R1_001.fastq.gz 13S1_S1_L002_R2_001.fastq.gz,fastq fastq,1633908192.0,10749396.0,E MTAB 9615:13S1 S1 L002 R,0:76 1:76,A:444126523;C:370832524;G:375586115;T:443096444;N:266586,76,76,,,444126523,370832524,375586115,443096444,266586,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94863,0.95255,0.11967,0.11346,0.6927,0.69566,0.48395,0.48478,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10042,ERR4648678,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L003_R1_001.fastq.gz 13S1_S1_L003_R2_001.fastq.gz,fastq fastq,1698133208.0,11171929.0,E MTAB 9615:13S1 S1 L003 R,0:76 1:76,A:461740823;C:385469489;G:390285009;T:460464431;N:173456,76,76,,,461740823,385469489,390285009,460464431,173456,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94875,0.95192,0.11914,0.11105,0.69353,0.69649,0.48055,0.48273,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10043,ERR4648679,ERX4572371,ERS5128751,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13S1,SAMEA7370301,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370301|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13S1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] +/+ or +/ |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13S1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13S1 p,13S1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] +/+ or +/ ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13S1_S1_L004_R1_001.fastq.gz 13S1_S1_L004_R2_001.fastq.gz,fastq fastq,1661636792.0,10931821.0,E MTAB 9615:13S1 S1 L004 R,0:76 1:76,A:451786646;C:377303854;G:381943974;T:450471337;N:130981,76,76,,,451786646,377303854,381943974,450471337,130981,ERX4572371,ERS5128751,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94966,0.95236,0.11837,0.11148,0.69215,0.6955,0.48615,0.48711,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10044,ERR4648672,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L001_R1_001.fastq.gz 13K6_S10_L001_R2_001.fastq.gz,fastq fastq,1697239752.0,11166051.0,E MTAB 9615:13K6 S10 L001 R,0:76 1:76,A:458337242;C:387675189;G:393817637;T:457129778;N:279906,76,76,,,458337242,387675189,393817637,457129778,279906,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94948,0.95219,0.12998,0.12293,0.67618,0.67848,0.50185,0.49952,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10045,ERR4648673,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L002_R1_001.fastq.gz 13K6_S10_L002_R2_001.fastq.gz,fastq fastq,1673328784.0,11008742.0,E MTAB 9615:13K6 S10 L002 R,0:76 1:76,A:451774513;C:382335962;G:388349370;T:450595018;N:273921,76,76,,,451774513,382335962,388349370,450595018,273921,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94837,0.95265,0.12834,0.12248,0.67515,0.67799,0.49985,0.50072,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10046,ERR4648674,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L003_R1_001.fastq.gz 13K6_S10_L003_R2_001.fastq.gz,fastq fastq,1718962376.0,11308963.0,E MTAB 9615:13K6 S10 L003 R,0:76 1:76,A:464326802;C:392820934;G:398719859;T:462921749;N:173032,76,76,,,464326802,392820934,398719859,462921749,173032,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94887,0.94779,0.12909,0.12199,0.67562,0.67777,0.49225,0.49141,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10047,ERR4648675,ERX4572370,ERS5128750,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K6,SAMEA7370300,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370300|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K6|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K6|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K6 p,13K6 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K6_S10_L004_R1_001.fastq.gz 13K6_S10_L004_R2_001.fastq.gz,fastq fastq,1700026824.0,11184387.0,E MTAB 9615:13K6 S10 L004 R,0:76 1:76,A:459161966;C:388439150;G:394446506;T:457846371;N:132831,76,76,,,459161966,388439150,394446506,457846371,132831,ERX4572370,ERS5128750,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9473,0.95161,0.12897,0.12179,0.67551,0.67811,0.48685,0.4972,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10048,ERR4648668,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L001_R1_001.fastq.gz 13K5_S6_L001_R2_001.fastq.gz,fastq fastq,1790254024.0,11777987.0,E MTAB 9615:13K5 S6 L001 R,0:76 1:76,A:487293594;C:405551734;G:411238332;T:485873462;N:296902,76,76,,,487293594,405551734,411238332,485873462,296902,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94726,0.94704,0.12004,0.11278,0.67533,0.67779,0.48364,0.48388,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10049,ERR4648669,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L002_R1_001.fastq.gz 13K5_S6_L002_R2_001.fastq.gz,fastq fastq,1749029952.0,11506776.0,E MTAB 9615:13K5 S6 L002 R,0:76 1:76,A:476215821;C:396276458;G:401611483;T:474647042;N:279148,76,76,,,476215821,396276458,401611483,474647042,279148,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.94762,0.95173,0.12006,0.11284,0.67631,0.68018,0.48241,0.47833,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10050,ERR4648670,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L003_R1_001.fastq.gz 13K5_S6_L003_R2_001.fastq.gz,fastq fastq,1811820544.0,11919872.0,E MTAB 9615:13K5 S6 L003 R,0:76 1:76,A:493339499;C:410551445;G:416118309;T:491625876;N:185415,76,76,,,493339499,410551445,416118309,491625876,185415,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9476,0.94796,0.12002,0.11151,0.67872,0.6802,0.47743,0.47744,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10051,ERR4648671,ERX4572369,ERS5128749,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K5,SAMEA7370299,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370299|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K5|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K5|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K5 p,13K5 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K5_S6_L004_R1_001.fastq.gz 13K5_S6_L004_R2_001.fastq.gz,fastq fastq,1774793800.0,11676275.0,E MTAB 9615:13K5 S6 L004 R,0:76 1:76,A:483347019;C:402198669;G:407461838;T:481643127;N:143147,76,76,,,483347019,402198669,407461838,481643127,143147,ERX4572369,ERS5128749,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.9475,0.95165,0.11907,0.11154,0.67734,0.67931,0.46812,0.48622,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10052,ERR4648664,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L001_R1_001.fastq.gz 13K1_S2_L001_R2_001.fastq.gz,fastq fastq,1668503392.0,10976996.0,E MTAB 9615:13K1 S2 L001 R,0:76 1:76,A:454536456;C:377057732;G:382495387;T:454135749;N:278068,76,76,,,454536456,377057732,382495387,454135749,278068,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95225,0.95532,0.12378,0.11159,0.70212,0.70317,0.49492,0.50085,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10053,ERR4648665,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L002_R1_001.fastq.gz 13K1_S2_L002_R2_001.fastq.gz,fastq fastq,1633824136.0,10748843.0,E MTAB 9615:13K1 S2 L002 R,0:76 1:76,A:444960536;C:369666363;G:374403909;T:444522641;N:270687,76,76,,,444960536,369666363,374403909,444522641,270687,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95199,0.95599,0.12228,0.11149,0.70151,0.70437,0.49885,0.49797,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10054,ERR4648666,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L003_R1_001.fastq.gz 13K1_S2_L003_R2_001.fastq.gz,fastq fastq,1692052752.0,11131926.0,E MTAB 9615:13K1 S2 L003 R,0:76 1:76,A:461375866;C:382427180;G:387578702;T:460499241;N:171763,76,76,,,461375866,382427180,387578702,460499241,171763,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95194,0.95208,0.1245,0.11189,0.701,0.70457,0.49831,0.49526,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10055,ERR4648667,ERX4572368,ERS5128748,ERP124248,PRJEB40594,scospondin mutant embryos,E-MTAB-9615,Transcriptome Analysis,Transcriptome comparison of scospondin mutants embryos with wild type siblings,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 09 30,,Protocols: Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,13K1,SAMEA7370298,Paris Brain Institute,ENA FIRST PUBLIC:2020 10 14T17:05:13Z|ENA LAST UPDATE:2020 09 30T20:50:27Z|External Id:SAMEA7370298|INSDC center name:Paris Brain Institute|INSDC first public:2020 10 14T17:05:13Z|INSDC last update:2020 09 30T20:50:27Z|INSDC status:public|Submitter Id:E MTAB 9615:13K1|age:48|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genetic modification:indel|genotype:scospondin[icm13] / |individual:30|organism part:whole organism|phenotype:curled|sample name:E MTAB 9615:13K1|scientific name:Danio rerio|sex:not available|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; scospondin mutant embryos,E MTAB 9615:13K1 p,13K1 p,scospondin mutant embryos,Anesthesia in water euthanasia and dissociation through seringe needle Trizol extraction isopropanol precipitation and RNAeasy column Qiagen KAPA mRNA HyperPrep Kit Roche,Experimental Factor: genotype:scospondin[icm13] / ,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP124248,NextSeq 500 paired end sequencing; scospondin mutant embryos,ENA FIRST PUBLIC:2020 10 14|ENA LAST UPDATE:2020 10 02,13K1_S2_L004_R1_001.fastq.gz 13K1_S2_L004_R2_001.fastq.gz,fastq fastq,1662467776.0,10937288.0,E MTAB 9615:13K1 S2 L004 R,0:76 1:76,A:453180833;C:375869158;G:380805111;T:452478416;N:134258,76,76,,,453180833,375869158,380805111,452478416,134258,ERX4572368,ERS5128748,ERA2937926,Paris Brain Institute|European Nucleotide Archive,Paris Brain Institute|European Nucleotide Archive,2,0.95157,0.95197,0.12307,0.11055,0.7027,0.70544,0.49989,0.49505,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,France,2020-09-30,Undetermined,Embryo,Whole Organism,All anatomical structures
10068,ERR4844843,ERX4714625,ERS5338302,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],wt rep2,SAMEA7579966,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579966|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep2|strain:Ab / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep2 s,wt rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep2.fastq.gz,fastq,3456340392.0,34221192.0,E MTAB 9777:wt rep2,0:101 1:0,A:850781866;C:827613239;G:837337477;T:936245388;N:4362422,101,0,,,850781866,827613239,837337477,936245388,4362422,ERX4714625,ERS5338302,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94198,,0.05681,,0.69613,,0.46685,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10069,ERR4844842,ERX4714624,ERS5338301,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],wt rep1,SAMEA7579965,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579965|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:wt rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:wt rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:wt rep1 s,wt rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,wt_rep1.fastq.gz,fastq,5640822932.0,55849732.0,E MTAB 9777:wt rep1,0:101 1:0,A:1394470185;C:1346058952;G:1354472388;T:1538701573;N:7119834,101,0,,,1394470185,1346058952,1354472388,1538701573,7119834,ERX4714624,ERS5338301,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94371,,0.05678,,0.69664,,0.47233,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10070,ERR4844841,ERX4714623,ERS5338300,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],foxk MO rep2,SAMEA7579964,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579964|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep2|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep2|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep2 s,foxk MO rep2 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep2.fastq.gz,fastq,3550070715.0,35149215.0,E MTAB 9777:foxk MO rep2,0:101 1:0,A:901160433;C:835963324;G:840839574;T:967604789;N:4502595,101,0,,,901160433,835963324,840839574,967604789,4502595,ERX4714623,ERS5338300,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.94006,,0.07603,,0.69455,,0.46867,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10071,ERR4844840,ERX4714622,ERS5338299,ERP125162,PRJEB41393,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E-MTAB-9777,Transcriptome Analysis,Foxk proteins are transcriptional regulators implicated in key biological processes such as glycolysis autophagy and cell cycle regulation among others. Here we employ targeted morpholino knockdown to deplete Foxk1 Fokx2 and Foxk2 1 proteins in developing zebrafish embryos. We demonstrate that the loss of Foxk transcription factors causes genome wide transcriptional misregulation characterised by upregulation of autophagy related genes and downregulation of cell cycle regulators. The phenotype is embryonic lethal with the majority of embryos not surviving past 24hpf.,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,,Protocols: Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],foxk MO rep1,SAMEA7579963,Garvan Institute of Medical Research,ENA first public:2020 12 01|ENA last update:2020 11 17|External Id:SAMEA7579963|INSDC center alias:Garvan Institute of Medical Research|INSDC center name:Garvan Institute of Medical Research|INSDC first public:2020 12 01T04:12:08Z|INSDC last update:2020 11 17T14:25:39Z|INSDC status:public|Submitter Id:E MTAB 9777:foxk MO rep1|age:24hpf|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|organism part:whole organism|sample name:E MTAB 9777:foxk MO rep1|strain:AB / Tubingen,,,,,,,,,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,E MTAB 9777:foxk MO rep1 s,foxk MO rep1 s,Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,Embryos were collected 0 hpf and incubated in 1X E3 medium 0.03% NaCl 0.005% CaCl2 0.0013% KCl 99.9557% H2O 0.008% H14MgO11S for 24 hours at 28.5°C Adult wild type AB/Tubingen Danio rerio zebrafish were bred in a 1 male:1 female ratio. 1c embryos were injected with morpholino oligonucleotides targeting foxk1 foxk2 and foxk2 1 transcripts Total RNA was purified from xxx embryos using the RNeasy Mini Kit Qiagen Valencia CA USA according to the manufacturer's instructions. mRNA Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 Illumina San Diego CA. Strand specific libraries were constructed using a dUTP methodology as described previously [Zhong S. et al. High Throughput Illumina Strand Specific RNA Sequencing Library Preparation. Cold Spring Harb. Protoc. 2011 940 949 2011],Experimental Factor: compound:morpholino against foxk1/foxk2/foxk2 1|Experimental Factor: dose:9,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 1500,,ERP125162,Illumina HiSeq 1500 sequencing; Depletion of Foxk transcription factors causes genome wide transcriptional misregulation and developmental arrest in zebrafish embryos,ENA FIRST PUBLIC:2020 12 01|ENA LAST UPDATE:2020 11 17,foxk1-2_rep1.fastq.gz,fastq,3601987139.0,35663239.0,E MTAB 9777:foxk MO rep1,0:101 1:0,A:910641017;C:846039018;G:853351642;T:987409698;N:4545764,101,0,,,910641017,846039018,853351642,987409698,4545764,ERX4714622,ERS5338299,ERA3145932,European Nucleotide Archive,European Nucleotide Archive,1,0.93784,,0.08061,,0.69292,,0.47364,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Unknown,2020-11-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
10309,ERR7179904,ERX6749461,ERS8138767,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate a highly potent synthetic corticosteroid which is known to have immunosuppressive effects on vertebrates including zebrafish was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate. In a modified version of the zebrafish embryo toxicity test OECD 236 20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf the eggs were manually dechorinated. At 48 hpf the embryos were immobilized by anaesthetization using 200 mg/mL tricaine. Using microinjection 8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4 0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 µL of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit© Agilent 5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,R1287,SAMEA10486022,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486022|INSDC center alias:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1287|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1287|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1287 s,R1287 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol. Standard flagellin from Bacillus subtilis 10% purity Pam3CSK4 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 L of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturers protocol. RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit Agilent 5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1287_sr.fastq.gz,fastq,2134815688.0,42280846.0,E MTAB 11092:R1287,0:50.49,A:565052096;C:502336362;G:482125031;T:582647501;N:2654698,50,,,,565052096,502336362,482125031,582647501,2654698,ERX6749461,ERS8138767,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9356,,0.11997,,0.68314,,0.47934,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10310,ERR7179903,ERX6749460,ERS8138766,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate a highly potent synthetic corticosteroid which is known to have immunosuppressive effects on vertebrates including zebrafish was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate. In a modified version of the zebrafish embryo toxicity test OECD 236 20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf the eggs were manually dechorinated. At 48 hpf the embryos were immobilized by anaesthetization using 200 mg/mL tricaine. Using microinjection 8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4 0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 µL of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit© Agilent 5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,R1284,SAMEA10486020,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486020|INSDC center alias:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1284|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1284|sex:mixed|stimulus:water|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1284 s,R1284 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol. Standard flagellin from Bacillus subtilis 10% purity Pam3CSK4 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 L of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturers protocol. RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit Agilent 5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,Experimental Factor: compound:Clobetasol propionate|Experimental Factor: dose:250|Experimental Factor: stimulus:water,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1284_sr.fastq.gz,fastq,2050986060.0,40612707.0,E MTAB 11092:R1284,0:50.50,A:538161680;C:490403596;G:466089424;T:554663872;N:1667488,50,,,,538161680,490403596,466089424,554663872,1667488,ERX6749460,ERS8138766,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.93753,,0.1231,,0.68479,,0.45919,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures
10311,ERR7179902,ERX6749459,ERS8138765,ERP132743,PRJEB48372,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E-MTAB-11092,Transcriptome Analysis,The aim of this experiment was to develop an approach for the assessment of immunotoxicity in zebrafish embryos Danio rerio using transcriptomic profiling. Clobetasol propionate a highly potent synthetic corticosteroid which is known to have immunosuppressive effects on vertebrates including zebrafish was used for continuous exposure from fertilization until extraction. As immunotoxicity can only be comprehensively assessed when the effect is observed during an acute infection the embryos were injected with a mixture of different pathogen associated molecular patterns PAMPs consisting of Pam3CSK4 synthetic lipopeptide polyI:C synthetic viral dsRNA and flagellin isolated from Bacillus subtilis. Functional gene expression analysis from samples obtained by different kinds and combinations of treatments in relation to appropriate controls is used to identify pathways that are upregulated by artificial infection and suppressed by treatment with clobetasol propionate. In a modified version of the zebrafish embryo toxicity test OECD 236 20 fertilized eggs were exposed to a sub lethal concentration 250 nM of clobetasol propionate for xxx hours under semi static conditions. The test comprised of three treatments with clobetasol propionate and two negative control NC groups and was performed in triplicates. At 46 hpf the eggs were manually dechorinated. At 48 hpf the embryos were immobilized by anaesthetization using 200 mg/mL tricaine. Using microinjection 8 nL of the mixed PAMPs 0.33 µg/mL Pam3CSK4 0.33 µg/mL polyI:C and 0.033 µg/mL flagellin were injected directly into the embryos bloodstream. One of each exposure groups was injected with PAMPs while another one was injected with ultrapure water to control for effects introduced by the injection process. One control group remained completely untreated. post injection the embryos were further incubated for 3 hours before 10 embryos were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit Macherey Nagel. RNA quality was assessed with a 2100 Bioanalyzer system Agilent before coding RNA was purified PolyA selection with TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq 4000 System Illumina in 50 bp single read mode. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25,,Protocols: For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the “Growth protocol”. For detailed information about exposure duration and conditions please refer to the “Treatment protocol”. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2°C on a 12:12 h light/dark cycle. They were fed daily with TetraMin® Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1°C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 µM in acetone before 500 µL were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 µL of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the “growth protocol”. Standard flagellin from Bacillus subtilis ≈ 10% purity Pam3CSK4 ≥ 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturer's instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 µL of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 µL PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 µm. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 µg/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24© MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturer's protocol. RNA concentration >100 ng/µl was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The sample's overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer© Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit© Agilent 5067 1511 according to the manufacturer's protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80°C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/µl total RNA at the sequencing facility “NGS Services for Integrative Genomics” at the University of Göttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,R1275,SAMEA10486018,"Fraunhofer Attract Eco'n'OMICs, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany",ENA first public:2022 01 01|ENA last update:2022 01 01|External Id:SAMEA10486018|INSDC center alias:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC center name:Fraunhofer Attract Eco'n'OMICs Fraunhofer Institute for Molecular Biology and Applied Ecology Schmallenberg Germany|INSDC first public:2022 01 01T00:13:13Z|INSDC last update:2022 01 01T00:13:13Z|INSDC status:public|Submitter Id:E MTAB 11092:R1275|age:51|broker name:ArrayExpress|common name:zebrafish|developmental stage:hatching long pec|genotype:wild type genotype|organism part:whole organism|replicate:T6|sample name:E MTAB 11092:R1275|sex:mixed|stimulus:PAMP|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,E MTAB 11092:R1275 s,R1275 s,Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,For each sample 10 zebrafish larvae were randomly picked from the glass well and carefully transferred to a 1.5 ml low binding Eppendorf tube. Once individuals were collected for all samples the supernatant was removed and the tubes were snap frozen in liquid nitrogen. For detailed information about embryonic incubation conditions and husbandry of adult broodstock please refer to the Growth protocol. For detailed information about exposure duration and conditions please refer to the Treatment protocol. Adult animal husbandry: Wild type zebrafish Danio rerio Strain AB broodstocks were maintained under flow through conditions in 150 L tanks at 26 +/ 2C on a 12:12 h light/dark cycle. They were fed daily with TetraMin Tetra Werke Melle Germany main feed ad libitum and nauplii of Artemia salina. The day before test start glass spawning trays with artificial substrate green glass beads stringed on stainless steel wire were placed at the bottom of each tank. post mating and spawning in the morning hours eggs were rinsed with clear Cu reduced water and placed into glass dishes for pre picking. Fish embryo incubation: For each sample 20 fertilized eggs in the early blastula stage were placed in glass petri dishes diameter 6 cm filled with 8 mL of the testing solution or control medium. Embryos were incubated at 27 +/ 1C on a 14:10 h light/dark cycle. At 24 hpf eggs were inspected while half of the test solution was renewed. Clobetasol propionate CAS: 25122 46 7 was purchased from Sigma Aldrich Taufkirchen Germany. For the test solution preparation first a 5 mM stock solution was prepared in Acetone 99.9% MS grade. This stock was diluted to 250 M in acetone before 500 L were added to a 500 mL DURAN glass bottle. To the bottle for the control solution only 500 L of pure Acetone was added. post complete evaporation of the acetone the bottle was filled up with 500 mL copper reduced tap water. Complete dissolution of precipitated clobetasol propionate was achieved by sonication for 30 minutes Sonorex RK 100H Bandelin Germany. The test solutions were freshly prepared one day prior the start of the experiment and were constantly aerated at room temperature. The glass wells for the incubation of the embryos were pre saturated with the respective test solution overnight and renewed at the beginning of the experiment. Per sample about 40 50 fertilized fish eggs were pre picked in glass petri dishes 10 cm diameter filled with 30 ml of the testing solution. Using an optical binokular microscope 20 embryos of the same early blastula stage were transferred from the pre picking plate into the test glass wells filled with 8 ml of the test solution. Embryos were then incubated as described in the growth protocol. Standard flagellin from Bacillus subtilis 10% purity Pam3CSK4 98 % purity and PolyI:C HMW high molecular weight were purchased from InvivoGen SAS Toulouse France. Stock solutions 1 mg/mL for polyI:C and Pam3CSK4; 0.1 mg/mL for flagellin were prepared in provided endotoxin free water aliquoted and stored according to the manufacturers instructions until further use. At approximately 46 hpf the embryos were manually dechorinated and then further incubated. A mixture of the different PAMPs was prepared by mixing 10 L of each component resulting in final concentrations of 0.33 mg/mL for polyI:C and Pam3CSK4 and 0.033 mg/mL for flagellin respectively. The device for microinjection was set up using FemtoTip II injection needles with a complementary universal capillary holder Eppendorf Hamburg Germany connected to an IM 300 microinjector Narishige London United Kingdom. Volume calibration was performed according to Sive et al. 2010 using a micrometer slide with 1/100 mm scale Bresser Rhede Germany. Briefly the needles were backfilled with 10 L PAMP mix or ultra pure water. Injections for volume calibration were made into a drop of immersion oil purred on the micrometer slide the output pressure was constantly kept at 10 psi while the time of injection was adjusted until an injected drop had a diameter of approximately 250 m. Assuming that the drop forms a perfect sphere this corresponds to a volume of about 8 nL. The procedure described below was performed for each of the five conditions in turn treating the three replicates simultaneously. In order to anaesthetize the embryos tricaine Sigma Aldrich Taufkirchen Germany stock solution 4 mg/mL in 21 mM Tris pH 9 was added to the petri dishes to a final concentration of 200 g/mL. The immobilized embryos were transferred onto a 1 % agarose plate which was divided into segments one for each replicate. Excess liquid was removed so that the embryos were kept in place by surface tension. Desiccation was prevented by adding liquid if needed. To ensure that the injections could be performed as quickly as possible the embryos were arranged in a row in a way that their dorsal sides pointed to the same direction. The puncture was made on the dorsal side of the yolk sac and the needle was advanced through the yolk until it reached the yolk sac circulation valley on the ventral side of the embryo where the injection was made directly into the bloodstream. post all replicates of a certain condition were processed the embryos were rinsed back into the corresponding dish containing renewed test solution. Total RNA was extracted using the NucleoSpin RNA/Protein kit from Macherey Nagel 740933.250 The pooled and snap frozen larvae were suspended in RP1 buffer and were transferred to a screw cap tubes filled with 0.3 g of Lysing Matrix D MP Biomedicals 6913050 ceramic beads. Tissue homogenization was performed at 5 m/s for 45 s with FastPrep 24 MP Biomedicals 6004500 at room temperature. From here on RNA was extracted according to the manufacturers protocol. RNA concentration >100 ng/l was measured using a Nanodrop 2000 spectrophotometer Thermo Scientific. The samples overall RNA quality and corresponding RIN value was fluorometrically determined with a 2100 Bioanalyzer Instrument system Agilent G2939BA using the Agilent RNA 6000 Nano Kit Agilent 5067 1511 according to the manufacturers protocol. Only samples with a RIN > 8 were used for downstream analysis. Samples were stored at 80C until they were send to the sequencing facility on dry ice. Sequencing libraries were prepared for each sample from 100 ng/l total RNA at the sequencing facility NGS Services for Integrative Genomics at the University of Gttingen in Germany. According to their standard workflow cDNA libraries were prepared from protein coding mRNA that were purified through PolyA selection using the TruSeq RNA Library Prep Kit v2 Illumina. Libraries were validated using a Fragment Analyzer system Agilent Santa Clara USA before sequencing.,Experimental Factor: compound:n1|Experimental Factor: stimulus:PAMP,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,ERP132743,Illumina HiSeq 4000 sequencing; Transcriptomic profiling of clobetasol propionate induced immunosuppression in challenged zebrafish embryos,ENA FIRST PUBLIC:2022 02 25|ENA LAST UPDATE:2022 02 25|loader:fastq load.py,p946sR1275_sr.fastq.gz,fastq,1157613512.0,22947522.0,E MTAB 11092:R1275,0:50.45,A:299754053;C:277899399;G:266613838;T:309994905;N:3351317,50,,,,299754053,277899399,266613838,309994905,3351317,ERX6749459,ERS8138765,ERA6860152,Fraunhofer Attract Eco,Fraunhofer Attract Eco,1,0.9411,,0.10048,,0.69008,,0.47233,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,Germany,2022-01-01,Hatching,Embryo,Whole Organism,All anatomical structures