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311 rows where devstage_curation_coarse = "Embryo" and experiment.library_selection = "PolyA"

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tissue_curation 6

devstage_curation 6

technology 4

experiment.library_strategy 3

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

experiment.library_selection 1

  • PolyA · 311 ✖

devstage_curation_coarse 1

  • Embryo · 311 ✖
Link 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 0 DRR314108 DRX303511 DRS233566 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of wild type sibling sample3 SAMD00399013   sample name:rna rw337 48hpf WT rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399013 DRX303511 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399013       23076492885.0 76679376.0 DRR314108 0:150.51 1:150.44 A:6146969533;C:5373690527;G:5458576301;T:6095818756;N:1437768 150 150     6146969533 5373690527 5458576301 6095818756 1437768 DRX303511 DRS233566 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.94223 0.94614 0.10721 0.10288 0.68745 0.68621 0.4728 0.47157 151 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
1 1 DRR314107 DRX303510 DRS233565 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of wild type sibling sample2 SAMD00399012   sample name:rna rw337 48hpf WT rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399012 DRX303510 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399012       26091623771.0 86694066.0 DRR314107 0:150.51 1:150.45 A:6955374552;C:6050013285;G:6169385096;T:6915281392;N:1569446 150 150     6955374552 6050013285 6169385096 6915281392 1569446 DRX303510 DRS233565 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.94028 0.94277 0.11038 0.10462 0.68288 0.68134 0.46992 0.47227 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
2 2 DRR314106 DRX303509 DRS233564 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of wild type sibling sample1 SAMD00399011   sample name:rna rw337 48hpf WT rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399011 DRX303509 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399011       23833525756.0 79191795.0 DRR314106 0:150.51 1:150.44 A:6324521565;C:5556755459;G:5694025045;T:6256748423;N:1475264 150 150     6324521565 5556755459 5694025045 6256748423 1475264 DRX303509 DRS233564 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.94723 0.94975 0.09521 0.09114 0.6776 0.67819 0.46045 0.46153 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
3 3 DRR314105 DRX303508 DRS233563 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of banp mutant sample3 SAMD00399010   sample name:rna rw337 48hpf Mutant rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399010 DRX303508 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399010       27688386114.0 92009317.0 DRR314105 0:150.49 1:150.44 A:7681451080;C:6071566134;G:6242782106;T:7690830655;N:1756139 150 150     7681451080 6071566134 6242782106 7690830655 1756139 DRX303508 DRS233563 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.91038 0.91556 0.17971 0.16967 0.67718 0.67716 0.47042 0.46425 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
4 4 DRR314104 DRX303507 DRS233562 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of banp mutant sample2 SAMD00399009   sample name:rna rw337 48hpf Mutant rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399009 DRX303507 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399009       22970994572.0 76322352.0 DRR314104 0:150.52 1:150.46 A:6142535654;C:5310453740;G:5430124468;T:6086516676;N:1364034 150 150     6142535654 5310453740 5430124468 6086516676 1364034 DRX303507 DRS233562 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.93707 0.94063 0.12175 0.11613 0.67825 0.67649 0.46485 0.46905 147 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
5 5 DRR314103 DRX303506 DRS233561 DRP008373 PRJDB12134 Comparison of expression profile between banp mutant and wildtype sibling. DRP008373 Other To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.       RNA seq of banp mutant sample1 SAMD00399008   sample name:rna rw337 48hpf Mutant rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00399008 DRX303506 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008373 Illumina NovaSeq 6000 paired end sequencing of SAMD00399008       23637901630.0 78541449.0 DRR314103 0:150.51 1:150.45 A:6359178134;C:5420730443;G:5530700546;T:6325864263;N:1428244 150 150     6359178134 5420730443 5530700546 6325864263 1428244 DRX303506 DRS233561 DRA012572 OIST|Developmental Neurobiology Unit Okinawa Institute of Science and Technology 2 0.9308 0.93545 0.13172 0.12462 0.68219 0.6814 0.46842 0.46984 150 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Japan 2022-04-01 Hatching Embryo Undetermined Embryo Imprecise
6 6 DRR315802 DRX305194 DRS231989 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       wildtype sibling sample4 SAMD00400823   sample name:rw147 2.5dpf wildtype rep 4|biological replicate:4                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400823 DRX305194 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400823       10262353995.0 34151547.0 DRR315802 0:150.27 1:150.22 A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550 150 150     2735078560 2386126821 2433638250 2707202814 307550 DRX305194 DRS231989 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95231 0.95295 0.09229 0.08773 0.71819 0.72107 0.46746 0.46617 151 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
7 7 DRR315801 DRX305193 DRS231988 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       wildtype sibling sample3 SAMD00400822   sample name:rw147 2.5dpf wildtype rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400822 DRX305193 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400822       11516368634.0 38355888.0 DRR315801 0:150.15 1:150.10 A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954 150 150     3080341643 2678048339 2713051368 3044449330 477954 DRX305193 DRS231988 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95353 0.95634 0.08909 0.08533 0.71374 0.71252 0.45986 0.46059 150 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
8 8 DRR315800 DRX305192 DRS231987 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       wildtype sibling sample2 SAMD00400821   sample name:rw147 2.5dpf wildtype rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400821 DRX305192 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400821       8814057148.0 29367513.0 DRR315800 0:150.09 1:150.04 A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957 150 150     2350403211 2054073465 2083044327 2326181188 354957 DRX305192 DRS231987 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95287 0.95643 0.0891 0.08586 0.70309 0.70252 0.46384 0.46281 151 149 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
9 9 DRR315799 DRX305191 DRS231986 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       wildtype sibling sample1 SAMD00400820   sample name:rw147 2.5dpf wildtype rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400820 DRX305191 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400820       10491955578.0 34900682.0 DRR315799 0:150.34 1:150.28 A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831 150 150     2796521111 2446218287 2483414564 2765477785 323831 DRX305191 DRS231986 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.9539 0.95646 0.08185 0.07808 0.70025 0.70013 0.44713 0.44987 150 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
10 10 DRR315798 DRX305190 DRS231985 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       strip1 mutant sample4 SAMD00400819   sample name:rw147 2.5dpf Mutant rep 4|biological replicate:4                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400819 DRX305190 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400819       9197802250.0 30604326.0 DRR315798 0:150.30 1:150.24 A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028 150 150     2468967963 2130949980 2158692262 2438931017 261028 DRX305190 DRS231985 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95159 0.95439 0.10146 0.09758 0.71995 0.71983 0.46519 0.46797 150 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
11 11 DRR315797 DRX305189 DRS231984 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       strip1 mutant sample3 SAMD00400818   sample name:rw147 2.5dpf Mutant rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400818 DRX305189 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400818       10498982078.0 34931731.0 DRR315797 0:150.31 1:150.25 A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945 150 150     2804535103 2445295179 2478768789 2770066062 316945 DRX305189 DRS231984 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95448 0.95652 0.0939 0.0887 0.71796 0.71847 0.46335 0.46615 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
12 12 DRR315796 DRX305188 DRS231983 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       strip1 mutant sample2 SAMD00400817   sample name:rw147 2.5dpf Mutant rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400817 DRX305188 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400817       9850145990.0 32782079.0 DRR315796 0:150.26 1:150.21 A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024 150 150     2636205537 2286508705 2319481100 2607600624 350024 DRX305188 DRS231983 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.95193 0.95472 0.09722 0.09375 0.7138 0.71299 0.45542 0.45994 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
13 13 DRR315795 DRX305187 DRS231982 DRP008318 PRJDB12206 Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes DRP008318 Transcriptome Analysis Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant "rw147" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.       strip1 mutant sample1 SAMD00400816   sample name:rw147 2.5dpf Mutant rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400816 DRX305187 1 1 1   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008318 Illumina NovaSeq 6000 paired end sequencing of SAMD00400816       9542039835.0 31780260.0 DRR315795 0:150.15 1:150.10 A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225 150 150     2543384204 2224374632 2258183435 2515655339 442225 DRX305187 DRS231982 DRA012640 OIST|Developmental Neurobiology Unit Developmental Neurobiology Unit 2 0.9528 0.95591 0.08656 0.0828 0.70352 0.70331 0.45316 0.44914 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
175 175 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
181 181 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> 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
303 303 DRR224539 DRX214824 DRS236347 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 48hpf C SAMD00222570   sample name:48hpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222570 DRX214824 48hpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222570       16828182200.0 84140911.0 DRR224539 0:100 1:100 A:3957959900;C:4467368792;G:4483580218;T:3919146988;N:126302 100 100     3957959900 4467368792 4483580218 3919146988 126302 DRX214824 DRS236347 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.97277 0.97115 0.05409 0.05185 0.76717 0.76836 0.46592 0.45571 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Hatching Embryo Fin Surface Structure
304 304 DRR224538 DRX214823 DRS236346 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 48hpf B SAMD00222569   sample name:48hpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222569 DRX214823 48hpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222569       22815822200.0 114079111.0 DRR224538 0:100 1:100 A:5651922913;C:5760379580;G:5844694518;T:5558658503;N:166686 100 100     5651922913 5760379580 5844694518 5558658503 166686 DRX214823 DRS236346 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96814 0.96379 0.03526 0.03362 0.71575 0.71697 0.47605 0.47359 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Hatching Embryo Fin Surface Structure
305 305 DRR224537 DRX214822 DRS236345 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 48hpf A SAMD00222568   sample name:48hpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222568 DRX214822 48hpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222568       13993230400.0 69966152.0 DRR224537 0:100 1:100 A:3484590137;C:3511805255;G:3624285719;T:3372446706;N:102583 100 100     3484590137 3511805255 3624285719 3372446706 102583 DRX214822 DRS236345 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96467 0.96428 0.04367 0.04212 0.72853 0.73125 0.49715 0.49652 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Hatching Embryo Fin Surface Structure
306 306 DRR224536 DRX214821 DRS236344 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 40hpf C SAMD00222567   sample name:40hpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222567 DRX214821 40hpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222567       14926054400.0 74630272.0 DRR224536 0:100 1:100 A:3647365116;C:3826172690;G:3866071867;T:3586333511;N:111216 100 100     3647365116 3826172690 3866071867 3586333511 111216 DRX214821 DRS236344 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96395 0.96168 0.05081 0.04957 0.75489 0.75607 0.51046 0.52135 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
307 307 DRR224535 DRX214820 DRS236343 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 40hpf B SAMD00222566   sample name:40hpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222566 DRX214820 40hpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222566       14413995800.0 72069979.0 DRR224535 0:100 1:100 A:3598207137;C:3642219692;G:3750145663;T:3423315835;N:107473 100 100     3598207137 3642219692 3750145663 3423315835 107473 DRX214820 DRS236343 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.97396 0.97107 0.04686 0.04549 0.7444 0.74968 0.50051 0.49798 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
308 308 DRR224534 DRX214819 DRS236342 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 40hpf A SAMD00222565   sample name:40hpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222565 DRX214819 40hpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222565       14351831800.0 71759159.0 DRR224534 0:100 1:100 A:3552114377;C:3639389412;G:3719404253;T:3440817088;N:106670 100 100     3552114377 3639389412 3719404253 3440817088 106670 DRX214819 DRS236342 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.96606 0.96569 0.04249 0.04107 0.7514 0.75367 0.49762 0.49753 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
309 309 DRR224533 DRX214818 DRS236341 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 32hpf C SAMD00222564   sample name:32hpf C                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222564 DRX214818 32hpf C 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222564       18499667800.0 92498339.0 DRR224533 0:100 1:100 A:4655671152;C:4605325822;G:4688156846;T:4550378341;N:135639 100 100     4655671152 4605325822 4688156846 4550378341 135639 DRX214818 DRS236341 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.9673 0.96864 0.04184 0.04008 0.73087 0.73318 0.48331 0.48043 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
310 310 DRR224532 DRX214817 DRS236340 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 32hpf B SAMD00222563   sample name:32hpf B                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222563 DRX214817 32hpf B 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222563       19952418000.0 99762090.0 DRR224532 0:100 1:100 A:4972665902;C:5012518349;G:5094132814;T:4872951533;N:149402 100 100     4972665902 5012518349 5094132814 4872951533 149402 DRX214817 DRS236340 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.97325 0.97252 0.03729 0.03575 0.71591 0.7163 0.47191 0.47859 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
311 311 DRR224531 DRX214816 DRS236339 DRP008458 PRJDB9741 RNA seq for developing pectoral fin in zebrafish DRP008458 Other From the developmental view of fin to limb transition an important event in vertebrate evolution we seek fish specific genes that show characteristic expression pattern in the developing fin.       pectoral fin bud from gM1116A zebrafish at 32hpf A SAMD00222562   sample name:32hpf A                 Illumina NovaSeq 6000 paired end sequencing of SAMD00222562 DRX214816 32hpf A 1 Illumina TruSeq Stranded mRNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP008458 Illumina NovaSeq 6000 paired end sequencing of SAMD00222562       16357024800.0 81785124.0 DRR224531 0:100 1:100 A:4049805675;C:4130985751;G:4172952730;T:4003159212;N:121432 100 100     4049805675 4130985751 4172952730 4003159212 121432 DRX214816 DRS236339 DRA010086 TOHOKUGL|Laboratory of organ morphogenesis Graduate School of Life Sciences, Tohoku University 2 0.97046 0.96886 0.03577 0.03489 0.73257 0.73231 0.4825 0.48849 100 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Japan 2022-04-21 Pharyngula Embryo Fin Surface Structure
9898 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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. … 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 So… 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 Ba… 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 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. … 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 So… 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 Ba… 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 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. … 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 So… 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 Ba… 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;