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34 rows where experiment.library_selection = "PolyA" and tissue_curation_coarse = "Embryo Imprecise"

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technology 2

tissue_curation_coarse 1

  • Embryo Imprecise · 34 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 34 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

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
36032 36032 SRR33405556 SRX28646822 SRS24917431 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         mut2 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant mut2 d2 mut2 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_mut-2_S6_R1_001.fastq.gz y680_mut-2_S6_R2_001.fastq.gz fastq fastq 13048391588.0 65176490.0 y680 mut 2 S6 R1 001.fastq.gz 0:100.12 1:100.08 A:3382606790;C:3166963239;G:3249911967;T:3247119183;N:1790409 100 100     3382606790 3166963239 3249911967 3247119183 1790409 SRX28646822 SRS24917431 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36033 36033 SRR33405557 SRX28646821 SRS24917430 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         mut1 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant mut1 d2 mut1 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_mut-1_S5_R1_001.fastq.gz y680_mut-1_S5_R2_001.fastq.gz fastq fastq 11244387522.0 56145229.0 y680 mut 1 S5 R1 001.fastq.gz 0:100.15 1:100.12 A:2893088657;C:2737659501;G:2830491662;T:2781546759;N:1600943 100 100     2893088657 2737659501 2830491662 2781546759 1600943 SRX28646821 SRS24917430 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36034 36034 SRR33405558 SRX28646820 SRS24917429 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         het4 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant het4 d2 het4 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_het-4_S4_R1_001.fastq.gz y680_het-4_S4_R2_001.fastq.gz fastq fastq 7488095202.0 37372687.0 y680 het 4 S4 R1 001.fastq.gz 0:100.20 1:100.16 A:1931359037;C:1813371312;G:1880760315;T:1861860377;N:744161 100 100     1931359037 1813371312 1880760315 1861860377 744161 SRX28646820 SRS24917429 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36035 36035 SRR33405559 SRX28646819 SRS24917428 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         het3 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant het3 d2 het3 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_het-3_S3_R1_001.fastq.gz y680_het-3_S3_R2_001.fastq.gz fastq fastq 13441009956.0 67072919.0 y680 het 3 S3 R1 001.fastq.gz 0:100.22 1:100.18 A:3484306615;C:3249847841;G:3351167195;T:3353988961;N:1699344 100 100     3484306615 3249847841 3351167195 3353988961 1699344 SRX28646819 SRS24917428 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36036 36036 SRR33405560 SRX28646818 SRS24917427 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         het2 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant het2 d2 het2 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_het-2_S2_R1_001.fastq.gz y680_het-2_S2_R2_001.fastq.gz fastq fastq 10048330828.0 50202819.0 y680 het 2 S2 R1 001.fastq.gz 0:100.10 1:100.05 A:2557623639;C:2473642678;G:2526118363;T:2490175343;N:770805 100 100     2557623639 2473642678 2526118363 2490175343 770805 SRX28646818 SRS24917427 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36037 36037 SRR33405561 SRX28646817 SRS24917426 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         het1 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:het|replicate:het 2 dpf replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant het1 d2 het1 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_het-1_S1_R1_001.fastq.gz y680_het-1_S1_R2_001.fastq.gz fastq fastq 21241485328.0 106063264.0 y680 het 1 S1 R1 001.fastq.gz 0:100.16 1:100.11 A:5428876256;C:5216202525;G:5316134708;T:5278092708;N:2179131 100 100     5428876256 5216202525 5316134708 5278092708 2179131 SRX28646817 SRS24917426 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36038 36038 SRR33405562 SRX28646816 SRS24917425 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         wt4 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant wt4 d2 wt4 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680-WT-4_S56_R1_001.fastq.gz y680-WT-4_S56_R2_001.fastq.gz fastq fastq 2871774704.0 14403351.0 y680 WT 4 S56 R1 001.fastq.gz 0:99.62 1:99.76 A:738963438;C:693060627;G:725455885;T:712804013;N:1490741 99 99     738963438 693060627 725455885 712804013 1490741 SRX28646816 SRS24917425 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36040 36040 SRR33405564 SRX28646814 SRS24917423 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         wt3 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant wt3 d2 wt3 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_WT-3_S11_R1_001.fastq.gz y680_WT-3_S11_R2_001.fastq.gz fastq fastq 4644100900.0 23208636.0 y680 WT 3 S11 R1 001.fastq.gz 0:100.02 1:100.08 A:1208863635;C:1115875593;G:1183409664;T:1134173818;N:1778190 100 100     1208863635 1115875593 1183409664 1134173818 1778190 SRX28646814 SRS24917423 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36049 36049 SRR33405573 SRX28646805 SRS24917414 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         mut4 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant mut4 d2 mut4 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_mut-4_S8_R1_001.fastq.gz y680_mut-4_S8_R2_001.fastq.gz fastq fastq 6364246187.0 31799210.0 y680 mut 4 S8 R1 001.fastq.gz 0:100.05 1:100.09 A:1644746630;C:1536469430;G:1617907325;T:1562993280;N:2129522 100 100     1644746630 1536469430 1617907325 1562993280 2129522 SRX28646805 SRS24917414 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36050 36050 SRR33405574 SRX28646804 SRS24917413 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         mut3 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:mut|replicate:mut 2 dpf replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant mut3 d2 mut3 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_mut-3_S7_R1_001.fastq.gz y680_mut-3_S7_R2_001.fastq.gz fastq fastq 12769594212.0 63754551.0 y680 mut 3 S7 R1 001.fastq.gz 0:100.17 1:100.12 A:3270488183;C:3128646350;G:3212521095;T:3156861188;N:1077396 100 100     3270488183 3128646350 3212521095 3156861188 1077396 SRX28646804 SRS24917413 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36051 36051 SRR33405575 SRX28646803 SRS24917412 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         wt2 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant wt2 d2 wt2 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680-WT-2_S40_R1_001.fastq.gz y680-WT-2_S40_R2_001.fastq.gz fastq fastq 7228768016.0 36426014.0 y680 WT 2 S40 R1 001.fastq.gz 0:99.18 1:99.27 A:1808349692;C:1804255213;G:1817770107;T:1795596464;N:2796540 99 99     1808349692 1804255213 1817770107 1795596464 2796540 SRX28646803 SRS24917412 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
36052 36052 SRR33405576 SRX28646802 SRS24917411 SRP582714 PRJNA1257950 Zebrafish Timothy syndrome knock in model PRJNA1257950 Other Characterization of transcriptomic changes in anterior tissue of zebrafish larvae with mutation in cacna1c to model Timothy sundrome.         wt1 d2   strain:ABC|age:2 dpf|collection date:2024 06|geo loc name:USA: Maryland Bethesda|sex:n/a|tissue:Anterior to swimbladder|genotype:WT|replicate:wt 2 dpf replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish TS2 mutant wt1 d2 wt1 d2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582714     y680_WT-1_S9_R1_001.fastq.gz y680_WT-1_S9_R2_001.fastq.gz fastq fastq 6639999850.0 33169283.0 y680 WT 1 S9 R1 001.fastq.gz 0:100.08 1:100.10 A:1706100512;C:1614640504;G:1665440844;T:1651930739;N:1887251 100 100     1706100512 1614640504 1665440844 1651930739 1887251 SRX28646802 SRS24917411 SRA2122396 NICHD|DDB NICHD                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   United States 2025-05-01 Hatching Embryo Undetermined Embryo Imprecise
59036 59036 SRR11578951 SRX8146805 SRS6509417 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     WT 54WT4 54WT4   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT4 R1 001.fastq.gz|filename2:54WT4 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54WT4 S7 S7 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54WT4_R2_001.fastq.gz 54WT4_R1_001.fastq.gz fastq fastq 7136583059.0 47328719.0 54WT4 R1 001.fastq.gz 0:75.39 1:75.40 A:1980254600;C:1593971374;G:1644375041;T:1916731613;N:1250431 75 75     1980254600 1593971374 1644375041 1916731613 1250431 SRX8146805 SRS6509417 SRA1067518 UPF|Genomics UPF 2 0.91504 0.91439 0.09602 0.09527 0.73245 0.73777 0.46955 0.48655 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59037 59037 SRR11578952 SRX8146804 SRS6509416 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     WT 54WT3 54WT3   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT3 R1 001.fastq.gz|filename2:54WT3 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54WT3 S5 S5 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54WT3_R1_001.fastq.gz 54WT3_R2_001.fastq.gz fastq fastq 5683476624.0 37713746.0 54WT3 R1 001.fastq.gz 0:75.35 1:75.35 A:1578885174;C:1271523804;G:1309222456;T:1522827535;N:1017655 75 75     1578885174 1271523804 1309222456 1522827535 1017655 SRX8146804 SRS6509416 SRA1067518 UPF|Genomics UPF 2 0.91126 0.91193 0.10356 0.10472 0.73975 0.7461 0.47619 0.47737 75 75 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59038 59038 SRR11578953 SRX8146803 SRS6509415 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     WT 54WT2 54WT2   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT2 R1 001.fastq.gz|filename2:54WT2 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54WT2 S3 S3 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54WT2_R1_001.fastq.gz 54WT2_R2_001.fastq.gz fastq fastq 6860136869.0 45523385.0 54WT2 R1 001.fastq.gz 0:75.34 1:75.35 A:1906640944;C:1530528609;G:1580010044;T:1841799217;N:1158055 75 75     1906640944 1530528609 1580010044 1841799217 1158055 SRX8146803 SRS6509415 SRA1067518 UPF|Genomics UPF 2 0.91215 0.91207 0.10861 0.11028 0.74381 0.74968 0.48908 0.49262 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59039 59039 SRR11578954 SRX8146802 SRS6509414 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     WT 54WT1 54WT1   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54WT1 R1 001.fastq.gz|filename2:54WT1 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54WT1 S1 S1 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54WT1_R1_001.fastq.gz 54WT1_R2_001.fastq.gz fastq fastq 6225284142.0 41319897.0 54WT1 R1 001.fastq.gz 0:75.33 1:75.33 A:1729358086;C:1392766589;G:1430690093;T:1671396108;N:1073266 75 75     1729358086 1392766589 1430690093 1671396108 1073266 SRX8146802 SRS6509414 SRA1067518 UPF|Genomics UPF 2 0.92733 0.92867 0.09387 0.09333 0.71163 0.71494 0.486 0.48867 72 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59040 59040 SRR11578955 SRX8146801 SRS6509413 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     Clo 54Clo4 54Clo4   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo4 R1 001.fastq.gz|filename2:54Clo4 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54Clo4 S8 S8 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54Clo4_R1_001.fastq.gz 54Clo4_R2_001.fastq.gz fastq fastq 6770856878.0 44915858.0 54Clo4 R1 001.fastq.gz 0:75.37 1:75.38 A:1876646232;C:1514408795;G:1561029116;T:1817557290;N:1215445 75 75     1876646232 1514408795 1561029116 1817557290 1215445 SRX8146801 SRS6509413 SRA1067518 UPF|Genomics UPF 2 0.91659 0.91674 0.10388 0.10458 0.71948 0.72523 0.48917 0.4856 76 74 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59041 59041 SRR11578956 SRX8146800 SRS6509412 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     Clo 54Clo3 54Clo3   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo3 R1 001.fastq.gz|filename2:54Clo3 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54Clo3 S6 S6 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54Clo3_R2_001.fastq.gz 54Clo3_R1_001.fastq.gz fastq fastq 5822390786.0 38650567.0 54Clo3 R1 001.fastq.gz 0:75.32 1:75.32 A:1619353584;C:1299190067;G:1337336722;T:1565486844;N:1023569 75 75     1619353584 1299190067 1337336722 1565486844 1023569 SRX8146800 SRS6509412 SRA1067518 UPF|Genomics UPF 2 0.91509 0.91425 0.10591 0.10604 0.76386 0.7693 0.46813 0.46524 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59042 59042 SRR11578957 SRX8146799 SRS6509411 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     Clo 54Clo2 54Clo2   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo2 R1 001.fastq.gz|filename2:54Clo2 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54Clo2 S4 S4 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54Clo2_R2_001.fastq.gz 54Clo2_R1_001.fastq.gz fastq fastq 6138626977.0 40727824.0 54Clo2 R1 001.fastq.gz 0:75.36 1:75.36 A:1700144556;C:1378599434;G:1420945150;T:1637894336;N:1043501 75 75     1700144556 1378599434 1420945150 1637894336 1043501 SRX8146799 SRS6509411 SRA1067518 UPF|Genomics UPF 2 0.90602 0.90662 0.09596 0.09691 0.75872 0.76274 0.48174 0.48196 75 75 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise
59043 59043 SRR11578958 SRX8146798 SRS6509410 SRP257662 PRJNA627095 Transcriptional profile of SAG neurod+ neuroblasts from clo mutant and sibling embryos at 54 hpf PRJNA627095 Other In many organs stem cell function depends on the communication with their niche partners. Cranial sensory neurons develop in close proximity to blood vessels however whether vasculature is an integral component of their niches is yet unknown. Here two separate novel roles for vasculature in cranial sensory neurogenesis in zebrafish are uncovered. The first involves a restrain of neuroblast proliferation at early stages. The second instead requires blood flow to trigger a transcriptional response which has been identified thanks to a RNAseq analysis. This transcriptional change modifies neuroblast metabolic status and induces sensory neuron differentiation. Altogether we demonstrate that the cranial vasculature constitutes a hitherto unrecognized niche component of the sensory ganglia that regulates the pace of their growth and differentiation dynamics.     Clo 54Clo1 54Clo1   strain:TgBACneurod:gfpnl1|age:54 hpf|sex:not applicable|tissue:SAG tissue|collection date:2018 11 14|geo loc name:Spain: Barcelona|lat lon:41.3851 N 2.1734 E|filename:54Clo1 R1 001.fastq.gz|filename2:54Clo1 R2 001.fastq.gz|BioSampleModel:Model organism or animal                 54Clo1 S2 S2 low input mRNA sequencing     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   SRP257662     54Clo1_R1_001.fastq.gz 54Clo1_R2_001.fastq.gz fastq fastq 7414571165.0 49175642.0 54Clo1 R1 001.fastq.gz 0:75.39 1:75.39 A:2056892212;C:1660481957;G:1708780731;T:1987161426;N:1254839 75 75     2056892212 1660481957 1708780731 1987161426 1254839 SRX8146798 SRS6509410 SRA1067518 UPF|Genomics UPF 2 0.90938 0.91029 0.1024 0.1024 0.73507 0.73852 0.48964 0.48917 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Unknown 2020-04-21 Hatching Embryo Undetermined Embryo Imprecise

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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");;