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run_metadata

66 rows where experiment.library_selection = "PCR", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Liver"

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technology 2

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Liver · 66 ✖

experiment.library_strategy 1

  • RNA-Seq · 66 ✖

experiment.library_source 1

experiment.library_selection 1

  • PCR · 66 ✖

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
28496 28496 SRR26321412 SRX22029502 SRS19102283 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 1 R27   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R27 R27 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R27.fastq fastq 23400.0 312.0 R27.fastq 0:75 A:7949;C:4612;G:4730;T:6100;N:9 75       7949 4612 4730 6100 9 SRX22029502 SRS19102283 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89642   0.06772   0.99827   0.75   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28497 28497 SRR26321413 SRX22029501 SRS19102284 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 4 R22   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R22 R22 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R22.fastq fastq 23400.0 312.0 R22.fastq 0:75 A:7470;C:4460;G:5063;T:6404;N:3 75       7470 4460 5063 6404 3 SRX22029501 SRS19102284 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87073   0.12167   0.99801   0.73157   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28498 28498 SRR26321414 SRX22029500 SRS19102281 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       R21 R21   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R21 R21 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R21.fastq fastq 23400.0 312.0 R21.fastq 0:75 A:7540;C:4349;G:4857;T:6646;N:8 75       7540 4349 4857 6646 8 SRX22029500 SRS19102281 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.8839   0.04494   0.99768   0.72769   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28499 28499 SRR26321415 SRX22029499 SRS19102282 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 2 R18   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R18 R18 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R18.fastq fastq 23400.0 312.0 R18.fastq 0:75 A:7380;C:4430;G:5069;T:6518;N:3 75       7380 4430 5069 6518 3 SRX22029499 SRS19102282 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87259   0.11196   0.99784   0.69791   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28500 28500 SRR26321416 SRX22029498 SRS19102280 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       1dpci 1 R17   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 1 dpci R17 R17 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R17.fastq fastq 23400.0 312.0 R17.fastq 0:75 A:7322;C:4455;G:5111;T:6507;N:5 75       7322 4455 5111 6507 5 SRX22029498 SRS19102280 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90439   0.12749   0.99813   0.71052   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28501 28501 SRR26321417 SRX22029497 SRS19102279 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 5 R1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R1 R1 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R1.fastq fastq 23400.0 312.0 R1.fastq 0:75 A:7934;C:4560;G:4922;T:5980;N:4 75       7934 4560 4922 5980 4 SRX22029497 SRS19102279 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87045   0.10526   0.99805   0.71978   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28502 28502 SRR26321418 SRX22029496 SRS19102277 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 4 R64   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R64 R64 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R64.fastq fastq 23400.0 312.0 R64.fastq 0:75 A:7844;C:4626;G:4804;T:6126;N:0 75       7844 4626 4804 6126 0 SRX22029496 SRS19102277 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90119   0.07509   0.99839   0.8   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28503 28503 SRR26321419 SRX22029495 SRS19102278 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 3 R61   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R61 R61 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R61.fastq fastq 23400.0 312.0 R61.fastq 0:75 A:7454;C:4556;G:4960;T:6425;N:5 75       7454 4556 4960 6425 5 SRX22029495 SRS19102278 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89098   0.06015   0.99813   0.77102   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28504 28504 SRR26321420 SRX22029494 SRS19102276 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 4 30   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci 30 30 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     30.fastq fastq 23400.0 312.0 30.fastq 0:75 A:7732;C:4528;G:5150;T:5987;N:3 75       7732 4528 5150 5987 3 SRX22029494 SRS19102276 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.88447   0.13147   0.99772   0.71584   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28505 28505 SRR26321421 SRX22029493 SRS19102275 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       R11 R11   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci R11 R11 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R11.fastq fastq 23400.0 312.0 R11.fastq 0:75 A:7818;C:4507;G:5107;T:5956;N:12 75       7818 4507 5107 5956 12 SRX22029493 SRS19102275 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.89345   0.11475   0.99847   0.82258   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28506 28506 SRR26321422 SRX22029492 SRS19102274 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 2 31   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci 31 31 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     31.fastq fastq 23400.0 312.0 31.fastq 0:75 A:7470;C:4619;G:4802;T:6504;N:5 75       7470 4619 4802 6504 5 SRX22029492 SRS19102274 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87699   0.11111   0.99829   0.78918   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28507 28507 SRR26321423 SRX22029491 SRS19102273 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       7dpci 1 R9   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 7 dpci R9 R9 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R9.fastq fastq 23400.0 312.0 R9.fastq 0:75 A:8130;C:4537;G:4809;T:5917;N:7 75       8130 4537 4809 5917 7 SRX22029491 SRS19102273 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.83588   0.05725   0.99801   0.68586   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28508 28508 SRR26321424 SRX22029490 SRS19102272 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 4 R33   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R33 R33 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R33.fastq fastq 23400.0 312.0 R33.fastq 0:75 A:7745;C:4421;G:4867;T:6360;N:7 75       7745 4421 4867 6360 7 SRX22029490 SRS19102272 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.87259   0.07335   0.99805   0.71428   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28509 28509 SRR26321425 SRX22029489 SRS19102271 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 3 R31   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R31 R31 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R31.fastq fastq 23400.0 312.0 R31.fastq 0:75 A:7441;C:4483;G:5163;T:6313;N:0 75       7441 4483 5163 6313 0 SRX22029489 SRS19102271 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.9   0.05925   0.9977   0.68325   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28510 28510 SRR26321426 SRX22029488 SRS19102270 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       3dpci 2 R29   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver 3 dpci R29 R29 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R29.fastq fastq 23400.0 312.0 R29.fastq 0:75 A:7379;C:4698;G:5166;T:6156;N:1 75       7379 4698 5166 6156 1 SRX22029488 SRS19102270 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.91016   0.05859   0.99797   0.74528   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28511 28511 SRR26321427 SRX22029487 SRS19102269 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury       SHAM 2 R62   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R62 R62 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R62.fastq fastq 23400.0 312.0 R62.fastq 0:75 A:7383;C:4566;G:4713;T:6728;N:10 75       7383 4566 4713 6728 10 SRX22029487 SRS19102269 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.91571   0.05363   0.99835   0.77674   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
28512 28512 SRR26321428 SRX22029486 SRS19102268 SRP465132 PRJNA1025903 Zebrafish cryoinjury regeneration Raw sequence reads PRJNA1025903 Whole Genome Sequencing Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury     Replicate 1 for SHAM SHAM 1 R63   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 RNA seq of zebrafish liver sham R63 R63 ham and injured livers at 1 3 and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition 3 adult zebrafish livers were pooled per tube discriminating between the injured border and liver tissue from other lobes. Finally 3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice with a plastic pestle to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M reads per sample.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA NextSeq 500   SRP465132     R63.fastq fastq 23400.0 312.0 R63.fastq 0:75 A:7516;C:4606;G:4765;T:6508;N:5 75       7516 4606 4765 6508 5 SRX22029486 SRS19102268 SRA1727674 Peter MacCallum Cancer Centre|Organogenesis and Cancer Peter MacCallum Cancer Centre 1 0.90385   0.0423   0.99805   0.72429   75   B   usable mapping rate illumina nextseq unknown random_priming unknown bulk bulk bulk   Australia 2023-10-11 Adult Adult Liver Liver and Biliary System
38290 38290 SRR1731762 SRX821156 SRS800969 SRP051449 PRJNA266270 Danio rerio Transcriptome or Gene expression PRJNA266270 Other To identify molecular signals that initiate liver regeneration post 1/3 PH         Transcriptome during early stage of liver regeneration post 1/3 PH   breed:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/3 partial hepatectomy D.rereios liver regeneration sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP051449     6h_run1_R1.fastq.gz 6h_run1_R2.fastq.gz fastq fastq 2014108128.0 13986862.0 6h 0:72 1:72 A:542840697;C:473739345;G:521450086;T:473979205;N:2098795 72 72     542840697 473739345 521450086 473979205 2098795 SRX821156 SRS800969 SRA220726 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.92698 0.90124 0.02898 0.0276 0.85141 0.85064 0.41793 0.40779 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
38291 38291 SRR1735290 SRX824451 SRS804070 SRP051556 PRJNA266272 Danio rerio Transcriptome or Gene expression PRJNA266272 Other To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH         transcriptome during liver regeneration post 1/9 PH   breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy D.rerios liver regeneration post 1/9 PH sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP051556     24h3_R1.fastq.gz 24h3_R2.fastq.gz fastq fastq 1569651120.0 10900355.0 24h3 0:72 1:72 A:423126744;C:367185056;G:396200408;T:381254240;N:1884672 72 72     423126744 367185056 396200408 381254240 1884672 SRX824451 SRS804070 SRA221177 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.93264 0.91624 0.03854 0.0375 0.81708 0.81554 0.43719 0.43414 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
38292 38292 SRR1735297 SRX824451 SRS804070 SRP051556 PRJNA266272 Danio rerio Transcriptome or Gene expression PRJNA266272 Other To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH         transcriptome during liver regeneration post 1/9 PH   breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy D.rerios liver regeneration post 1/9 PH sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP051556     168h1_R1.fastq.gz 168h1_R2.fastq.gz fastq fastq 2340104400.0 16250725.0 168h1 0:72 1:72 A:667910990;C:526343343;G:603352668;T:540093539;N:2403860 72 72     667910990 526343343 603352668 540093539 2403860 SRX824451 SRS804070 SRA221177 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.9275 0.90676 0.03565 0.03486 0.85456 0.85421 0.42251 0.42133 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
44037 44037 SRR6232243 SRX3340673 SRS2642293 SRP122564 PRJNA416165 liver RNA squence PRJNA416165 Metagenomics Raw sequence reads of liver RNA of four treatment       C 1   strain:not applicable|isolate:liver sample|breed:Nile tilapia|cultivar:not applicable|ecotype:missing|age:4 month|dev stage:not collected|sex:female|tissue:liver|collection date:2014 10|treatment:control|BioSampleModel:Model organism or animal                 C C C liver RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP122564     13_ATCACG_L004_R2_001.fastq.gz 13_ATCACG_L004_R1_001.fastq.gz fastq fastq 4006393272.0 15898386.0 13 ATCACG L004 R1 001.fastq.gz 0:126 1:126 A:1095412221;C:911994717;G:928631129;T:1069381941;N:973264 126 126     1095412221 911994717 928631129 1069381941 973264 SRX3340673 SRS2642293 SRA625810 East China Normal University|LANEH East China Normal University 2 0.94763 0.94617 0.04358 0.04466 0.83597 0.83564 0.49418 0.48966 126 126 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2018-01-01 Adult Adult Liver Liver and Biliary System
44038 44038 SRR6232244 SRX3340672 SRS2642292 SRP122564 PRJNA416165 liver RNA squence PRJNA416165 Metagenomics Raw sequence reads of liver RNA of four treatment       F 2   strain:not applicable|isolate:liver sample|breed:Nile tilapia|cultivar:not applicable|ecotype:missing|age:4 month|dev stage:not collected|sex:female|tissue:liver|collection date:2014 10|treatment:fasting|BioSampleModel:Model organism or animal                 S S S liver RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP122564     19_CGATGT_L004_R1_001.fastq.gz 19_CGATGT_L004_R2_001.fastq.gz fastq fastq 3329356968.0 13211734.0 19 CGATGT L004 R2 001.fastq.gz 0:126 1:126 A:869750034;C:796186215;G:810918586;T:851683226;N:818907 126 126     869750034 796186215 810918586 851683226 818907 SRX3340672 SRS2642292 SRA625810 East China Normal University|LANEH East China Normal University 2 0.95382 0.95299 0.03317 0.03453 0.79024 0.79271 0.45786 0.44921 126 126 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2018-01-01 Adult Adult Liver Liver and Biliary System
44039 44039 SRR6232245 SRX3340671 SRS2642291 SRP122564 PRJNA416165 liver RNA squence PRJNA416165 Metagenomics Raw sequence reads of liver RNA of four treatment       CL 3   strain:not applicable|isolate:liver sample|breed:Nile tilapia|cultivar:not applicable|ecotype:missing|age:4 month|dev stage:not collected|sex:female|tissue:liver|collection date:2014 10|treatment:control in low temperature|BioSampleModel:Model organism or animal                 CL CL CL liver RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP122564     30_TTAGGC_L004_R1_001.fastq.gz 30_TTAGGC_L004_R2_001.fastq.gz fastq fastq 4476914064.0 17765532.0 30 TTAGGC L004 R1 001.fastq.gz 0:126 1:126 A:1209409451;C:1033074528;G:1051420241;T:1181919392;N:1090452 126 126     1209409451 1033074528 1051420241 1181919392 1090452 SRX3340671 SRS2642291 SRA625810 East China Normal University|LANEH East China Normal University 2 0.94215 0.94059 0.06325 0.06581 0.82582 0.82625 0.57851 0.59911 126 126 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2018-01-01 Adult Adult Liver Liver and Biliary System
44040 44040 SRR6232246 SRX3340670 SRS2642290 SRP122564 PRJNA416165 liver RNA squence PRJNA416165 Metagenomics Raw sequence reads of liver RNA of four treatment       FL 4   strain:not applicable|isolate:liver sample|breed:Nile tilapia|cultivar:not applicable|ecotype:missing|age:4 month|dev stage:not collected|sex:female|tissue:liver|collection date:2014 10|treatment:fasting in low temperature|BioSampleModel:Model organism or animal                 SL SL SL liver RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina MiSeq   SRP122564     33_TGACCA_L004_R2_001.fastq.gz 33_TGACCA_L004_R1_001.fastq.gz fastq fastq 4550986692.0 18059471.0 33 TGACCA L004 R1 001.fastq.gz 0:126 1:126 A:1207283315;C:1072491999;G:1095805633;T:1174315833;N:1089912 126 126     1207283315 1072491999 1095805633 1174315833 1089912 SRX3340670 SRS2642290 SRA625810 East China Normal University|LANEH East China Normal University 2 0.94238 0.94022 0.05267 0.05506 0.8492 0.84881 0.56045 0.56064 126 126 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2017-10-28 Adult Adult Liver Liver and Biliary System
50742 50742 SRR8293702 SRX5108304 SRS4117717 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       SMPs 2 SMPs 2   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 SMPs 2 SMPs 2 SMPs 2 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Mp1R2_20180118_GCTCGG_S22_L002_R1_001.fastq.gz Mp1R2_20180118_GCTCGG_S22_L002_R2_001.fastq.gz fastq fastq 16320012956.0 54039778.0 Mp1R2 20180118 GCTCGG S22 L002 R1 001.fastq.gz 0:151 1:151 A:4258032240;C:3874227665;G:4062515446;T:4124455523;N:782082 151 151     4258032240 3874227665 4062515446 4124455523 782082 SRX5108304 SRS4117717 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95472 0.9625 0.02416 0.02281 0.84313 0.84916 0.38914 0.38276 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50743 50743 SRR8293703 SRX5108303 SRS4117716 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       SMPs 1 SMPs 1   strain:AB|age:18 wpf|dev stage:maturity|sex:missing|tissue:liver|BioSampleModel:Model organism or animal                 SMPs 1 SMPs 1 SMPs 1 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Mp1R1_20180118_GCTAAC_S21_L002_R1_001.fastq.gz Mp1R1_20180118_GCTAAC_S21_L002_R2_001.fastq.gz fastq fastq 15896306956.0 52636778.0 Mp1R1 20180118 GCTAAC S21 L002 R1 001.fastq.gz 0:151 1:151 A:4143450650;C:3789612315;G:3961854759;T:4000619639;N:769593 151 151     4143450650 3789612315 3961854759 4000619639 769593 SRX5108303 SRS4117716 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96393 0.96777 0.02141 0.01948 0.84662 0.85194 0.32349 0.31721 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50744 50744 SRR8293704 SRX5108302 SRS4117715 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu 3 Cu 3   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 Cu 3 Cu 3 Cu 3 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Me1R3_20180118_GCGAGT_S66_L005_R1_001.fastq.gz Me1R3_20180118_GCGAGT_S66_L005_R2_001.fastq.gz fastq fastq 8744057264.0 28953832.0 Me1R3 20180118 GCGAGT S66 L005 R1 001.fastq.gz 0:151 1:151 A:2285359674;C:2075565607;G:2170998901;T:2211924322;N:208760 151 151     2285359674 2075565607 2170998901 2211924322 208760 SRX5108302 SRS4117715 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96069 0.96777 0.023 0.02065 0.84867 0.85066 0.32219 0.31787 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50745 50745 SRR8293705 SRX5108301 SRS4117714 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu 2 Cu 2   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 Cu 2 Cu 2 Cu 2 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Me1R2_20180118_GCCACA_S65_L005_R1_001.fastq.gz Me1R2_20180118_GCCACA_S65_L005_R2_001.fastq.gz fastq fastq 7289258334.0 24136617.0 Me1R2 20180118 GCCACA S65 L005 R1 001.fastq.gz 0:151 1:151 A:1905718804;C:1735066763;G:1809040423;T:1839260934;N:171410 151 151     1905718804 1735066763 1809040423 1839260934 171410 SRX5108301 SRS4117714 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.9672 0.97084 0.02592 0.02251 0.85374 0.85606 0.2849 0.2921 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50746 50746 SRR8293706 SRX5108300 SRS4117713 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu 1 Cu 1   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 Cu 1 Cu 1 Cu 1 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Me1R1_20180118_GATAGA_S52_L004_R1_001.fastq.gz Me1R1_20180118_GATAGA_S52_L004_R2_001.fastq.gz fastq fastq 7752702702.0 25671201.0 Me1R1 20180118 GATAGA S52 L004 R1 001.fastq.gz 0:151 1:151 A:2033639697;C:1835495127;G:1926587351;T:1956737427;N:243100 151 151     2033639697 1835495127 1926587351 1956737427 243100 SRX5108300 SRS4117713 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95745 0.96286 0.02672 0.02479 0.84127 0.84394 0.32904 0.3349 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50747 50747 SRR8293707 SRX5108299 SRS4117711 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       control3 control3   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 control3 control3 control3 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Ck1R3_20180118_GCCAAG_S51_L004_R1_001.fastq.gz Ck1R3_20180118_GCCAAG_S51_L004_R2_001.fastq.gz fastq fastq 7740741388.0 25631594.0 Ck1R3 20180118 GCCAAG S51 L004 R1 001.fastq.gz 0:151 1:151 A:2024940989;C:1841313648;G:1923087030;T:1951153220;N:246501 151 151     2024940989 1841313648 1923087030 1951153220 246501 SRX5108299 SRS4117711 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95818 0.96298 0.02164 0.0204 0.84975 0.8521 0.31057 0.30266 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50748 50748 SRR8293708 SRX5108298 SRS4117712 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       control2 control2   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 control2 control2 control2 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Ck1R2_20180118_GATGAA_S50_L004_R2_001.fastq.gz Ck1R2_20180118_GATGAA_S50_L004_R1_001.fastq.gz fastq fastq 7416922492.0 24559346.0 Ck1R2 20180118 GATGAA S50 L004 R1 001.fastq.gz 0:151 1:151 A:1945820357;C:1753174282;G:1834367593;T:1883320166;N:240094 151 151     1945820357 1753174282 1834367593 1883320166 240094 SRX5108298 SRS4117712 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96201 0.96662 0.0255 0.02257 0.84932 0.85147 0.26151 0.25494 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2018-12-09 Adult Adult Liver Liver and Biliary System
50749 50749 SRR8293709 SRX5108297 SRS4117710 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       control1 control   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 control1 control1 control1 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Ck1R1_20180118_GAGTTA_S49_L004_R2_001.fastq.gz Ck1R1_20180118_GAGTTA_S49_L004_R1_001.fastq.gz fastq fastq 8229766062.0 27250881.0 Ck1R1 20180118 GAGTTA S49 L004 R1 001.fastq.gz 0:151 1:151 A:2152325113;C:1947656575;G:2050467497;T:2079055596;N:261281 151 151     2152325113 1947656575 2050467497 2079055596 261281 SRX5108297 SRS4117710 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95887 0.96418 0.02339 0.02103 0.83433 0.83652 0.33034 0.3273 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2018-12-09 Adult Adult Liver Liver and Biliary System
50750 50750 SRR8293710 SRX5108296 SRS4117709 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPs 1 Cu+SMPs 1   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPs 1 Cu+SMPs 1 Cu+SMPs 1 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     m1R1_20180118_GGTGCG_S67_L005_R1_001.fastq.gz m1R1_20180118_GGTGCG_S67_L005_R2_001.fastq.gz fastq fastq 7261435376.0 24044488.0 m1R1 20180118 GGTGCG S67 L005 R1 001.fastq.gz 0:151 1:151 A:1891573260;C:1727429677;G:1810549537;T:1831709558;N:173344 151 151     1891573260 1727429677 1810549537 1831709558 173344 SRX5108296 SRS4117709 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96212 0.96826 0.02408 0.02176 0.85253 0.85458 0.32893 0.33018 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50751 50751 SRR8293711 SRX5108295 SRS4117708 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       SMPs 3 SMPs 3   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 SMPs 3 SMPs 3 SMPs 3 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     Mp1R3_20180119_GGAGAA_S40_L002_R1_001.fastq.gz Mp1R3_20180119_GGAGAA_S40_L002_R2_001.fastq.gz fastq fastq 7444548546.0 24650823.0 Mp1R3 20180119 GGAGAA S40 L002 R1 001.fastq.gz 0:151 1:151 A:1960577865;C:1757726179;G:1847580914;T:1878405296;N:258292 151 151     1960577865 1757726179 1847580914 1878405296 258292 SRX5108295 SRS4117708 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95847 0.96668 0.02048 0.01983 0.84904 0.85117 0.27954 0.30365 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50752 50752 SRR8293712 SRX5108294 SRS4117707 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPsN 3 Cu+SMPsN 3   strain:AB|age:18 wpf|dev stage:maturity|sex:pooled male and female|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPsN 3 Cu+SMPsN 3 Cu+SMPsN 3 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     n1R3_20180119_TAGGAT_S44_L002_R1_001.fastq.gz n1R3_20180119_TAGGAT_S44_L002_R2_001.fastq.gz fastq fastq 10656896876.0 35287738.0 n1R3 20180119 TAGGAT S44 L002 R1 001.fastq.gz 0:151 1:151 A:2806256809;C:2508185673;G:2638315646;T:2703769987;N:368761 151 151     2806256809 2508185673 2638315646 2703769987 368761 SRX5108294 SRS4117707 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96152 0.96695 0.02413 0.02141 0.85133 0.85376 0.29313 0.28874 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50753 50753 SRR8293713 SRX5108293 SRS4117706 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPs 3 Cu+SMPs 3   strain:AB|age:18 wpf|dev stage:maturity|sex:pooled male and female|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPs 3 Cu+SMPs 3 Cu+SMPs 3 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     m1R3_20180119_GTCGTA_S41_L002_R1_001.fastq.gz m1R3_20180119_GTCGTA_S41_L002_R2_001.fastq.gz fastq fastq 6697412022.0 22176861.0 m1R3 20180119 GTCGTA S41 L002 R1 001.fastq.gz 0:151 1:151 A:1739063802;C:1600622113;G:1686365017;T:1671128002;N:233088 151 151     1739063802 1600622113 1686365017 1671128002 233088 SRX5108293 SRS4117706 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95032 0.95944 0.01941 0.01924 0.86168 0.8636 0.47268 0.47686 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50754 50754 SRR8293714 SRX5108292 SRS4117705 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPs 2 Cu+SMPs 2   strain:AB|age:18 wpf|dev stage:maturity|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPs 2 Cu+SMPs 2 Cu+SMPs 2 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     m1R2_20180118_GTACGC_S68_L005_R1_001.fastq.gz m1R2_20180118_GTACGC_S68_L005_R2_001.fastq.gz fastq fastq 9015120384.0 29851392.0 m1R2 20180118 GTACGC S68 L005 R1 001.fastq.gz 0:151 1:151 A:2350451639;C:2147730897;G:2239810671;T:2276917297;N:209880 151 151     2350451639 2147730897 2239810671 2276917297 209880 SRX5108292 SRS4117705 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95809 0.96489 0.0238 0.02355 0.84551 0.84881 0.37797 0.36352 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50755 50755 SRR8293715 SRX5108291 SRS4117704 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPsN 2 Cu+SMPsN 2   strain:AB|age:18 wpf|dev stage:maturity|sex:pooled male and female|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPsN 2 Cu+SMPsN 2 Cu+SMPsN 2 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     n1R2_20180119_GTGTTC_S43_L002_R1_001.fastq.gz n1R2_20180119_GTGTTC_S43_L002_R2_001.fastq.gz fastq fastq 7676119126.0 25417613.0 n1R2 20180119 GTGTTC S43 L002 R1 001.fastq.gz 0:151 1:151 A:1992270681;C:1831330491;G:1922009670;T:1930242322;N:265962 151 151     1992270681 1831330491 1922009670 1930242322 265962 SRX5108291 SRS4117704 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.95476 0.9616 0.02405 0.02228 0.81996 0.82256 0.38924 0.3984 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
50756 50756 SRR8293716 SRX5108290 SRS4117703 SRP172922 PRJNA509052 SMPs+NOM+Cu PRJNA509052 Other Polystyrene Microplastics as a Vector for Copper Exposure in Zebrafish Danio rerio: Impacts of Natural Organic Matter on Accumulation and Toxic Effects       Cu+SMPsN 1 Cu+SMPsN 1   strain:AB|age:18 wpf|dev stage:maturity|sex:pooled male and female|tissue:liver|BioSampleModel:Model organism or animal                 Cu+SMPsN 1 Cu+SMPsN 1 Cu+SMPsN 1 Danio rerio liver     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP172922     n1R1_20180119_GTCTGT_S42_L002_R1_001.fastq.gz n1R1_20180119_GTCTGT_S42_L002_R2_001.fastq.gz fastq fastq 9536718476.0 31578538.0 n1R1 20180119 GTCTGT S42 L002 R1 001.fastq.gz 0:151 1:151 A:2495081179;C:2260669897;G:2361458799;T:2419177239;N:331362 151 151     2495081179 2260669897 2361458799 2419177239 331362 SRX5108290 SRS4117703 SRA820198 Nanjing University|School of the Environment Nanjing University 2 0.96565 0.96896 0.02065 0.01883 0.84831 0.851 0.25795 0.27663 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-08 Adult Adult Liver Liver and Biliary System
62854 62854 SRR13440556 SRX9853978 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO GD 4 DIO GD 4 DIO with GD treatment     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO_GD-4 fastq 4457846127.0 35434325.0 DIO GD 4 0:125.81 A:1132283216;C:1070720177;G:1157322546;T:1097520188;N:0 125       1132283216 1070720177 1157322546 1097520188 0 SRX9853978 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.61358   0.13617   0.87896   0.27516   178   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62855 62855 SRR13440557 SRX9853977 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO GD 3 DIO GD 3 DIO with GD treatment     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO_GD-3 fastq 2209140756.0 21626130.0 DIO GD 3 0:102.15 A:583812333;C:487262915;G:584943625;T:553121883;N:0 102       583812333 487262915 584943625 553121883 0 SRX9853977 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.63225   0.1658   0.86379   0.37214   92   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62856 62856 SRR13440558 SRX9853976 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO GD 2 DIO GD 2 DIO with GD treatment     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO_GD-2 fastq 1777323103.0 18933651.0 DIO GD 2 0:93.87 A:464601836;C:413760770;G:460577599;T:438382898;N:0 93       464601836 413760770 460577599 438382898 0 SRX9853976 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.65849   0.15297   0.84135   0.3349   101   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62857 62857 SRR13440559 SRX9853975 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO GD 1 DIO GD 1 DIO with GD treatment     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO_GD-1 fastq 3107066238.0 25095995.0 DIO GD 1 0:123.81 A:793240480;C:738189877;G:777063754;T:798572127;N:0 123       793240480 738189877 777063754 798572127 0 SRX9853975 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.7426   0.17704   0.89051   0.25099   52   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62858 62858 SRR13440560 SRX9853974 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO 4 DIO 4 Diet incuced obesity DIO     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO-4 fastq 2329004075.0 20271175.0 DIO 4 0:114.89 A:567452533;C:570566957;G:621549245;T:569435340;N:0 114       567452533 570566957 621549245 569435340 0 SRX9853974 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.84548   0.27189   0.86198   0.45426   122   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62859 62859 SRR13440561 SRX9853973 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO 3 DIO 3 Diet incuced obesity DIO     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO-3 fastq 2346162628.0 19400931.0 DIO 3 0:120.93 A:579812559;C:570332195;G:613738317;T:582279557;N:0 120       579812559 570332195 613738317 582279557 0 SRX9853973 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.78629   0.25304   0.89041   0.35231   150   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-14 Adult Adult Liver Liver and Biliary System
62860 62860 SRR13440562 SRX9853972 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO 2 DIO 2 Diet incuced obesity DIO     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO-2 fastq 3553599859.0 32601495.0 DIO 2 0:109.00 A:888818483;C:851068166;G:947933039;T:865780171;N:0 109       888818483 851068166 947933039 865780171 0 SRX9853972 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.86167   0.31911   0.86206   0.66264   174   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-20 Adult Adult Liver Liver and Biliary System
62861 62861 SRR13440563 SRX9853971 SRS8035408 SRP301838 PRJNA691414 Transcriptomic analysis of GD treated zebrafish liver PRJNA691414 Other Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.       Zebrafish liver from AB strain GD DIO Zebrafish   strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: adult female liver DIO 1 DIO 1 Diet incuced obesity DIO     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ION_TORRENT Ion Torrent Proton   SRP301838     DIO-1 fastq 2554201974.0 21594302.0 DIO 1 0:118.28 A:631716258;C:620459753;G:664379409;T:637646554;N:0 118       631716258 620459753 664379409 637646554 0 SRX9853971 SRS8035408 SRA1184195 Mie University|Graduate School of Regional Innovation Studies Mie University 1 0.77174   0.21322   0.89962   0.33158   240   B   usable mapping rate ion_torrent ion_torrent unknown random_priming unknown bulk unknown unknown   Japan 2021-01-20 Adult Adult Liver Liver and Biliary System
63376 63376 SRR13760196 SRX10146924 SRS8299540 SRP307421 PRJNA703759 Danio rerio transcriptome analysis PRJNA703759 Transcriptome Analysis Differential analysis of Chlorpyrifos treatment effect in liver tissue       E Sample E   strain:not applicable|age:5 month|dev stage:Adult|sex:not applicable|tissue:Liver|collected by:Bestha Lakshmi|treatment:Chlorpyrifos|BioSampleModel:Model organism or animal                 E Sample E Sample E Total RNA sequencing     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP307421     F00118317-E_S39_1.fastq.gz F00118317-E_S39_2.fastq.gz fastq fastq 4198034352.0 13900776.0 F00118317 E S39 1.fastq.gz 0:151 1:151 A:1144870642;C:939226318;G:991368510;T:1122322391;N:246491 151 151     1144870642 939226318 991368510 1122322391 246491 SRX10146924 SRS8299540 SRA1198573 Sri Krishnadevaraya University|Microbiology Sri Krishnadevaraya University 2 0.6473 0.61397 0.05462 0.0481 0.83071 0.83609 0.45852 0.46791 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   India 2021-02-22 Adult Adult Liver Liver and Biliary System
63377 63377 SRR13760197 SRX10146923 SRS8299539 SRP307421 PRJNA703759 Danio rerio transcriptome analysis PRJNA703759 Transcriptome Analysis Differential analysis of Chlorpyrifos treatment effect in liver tissue       C Sample C   strain:not applicable|age:5 month|dev stage:Adult|sex:not applicable|tissue:Liver|collected by:Bestha Lakshmi|BioSampleModel:Model organism or animal                 S Sample C Sample C Total RNA sequencing     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP307421     F00118315-C_S38_1.fastq.gz F00118315-C_S38_2.fastq.gz fastq fastq 5486090022.0 18165861.0 F00118315 C S38 1.fastq.gz 0:151 1:151 A:1472935581;C:1252693566;G:1317674077;T:1442470847;N:315951 151 151     1472935581 1252693566 1317674077 1442470847 315951 SRX10146923 SRS8299539 SRA1198573 Sri Krishnadevaraya University|Microbiology Sri Krishnadevaraya University 2 0.7043 0.66918 0.03223 0.02933 0.8762 0.88022 0.24737 0.24236 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   India 2021-02-22 Adult Adult Liver Liver and Biliary System
70432 70432 SRR19831099 SRX15874807 SRS13564513 SRP383398 PRJNA851939 Danio rerio breed:Wild type Transcriptome or Gene expression PRJNA851939 Other Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       M3FL M3FL   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:Adult|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 M3 female Dre M3 female Dre M3 female Briefly one RNA pool of 5 livers n=1 from each treatment and sex with a minimum concentration of 40 ng/L were subjected to a quality control to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic USA; integrity and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina USA. Subsequently sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand post which a custom second strand synthesis buffer Illumina USA as well as dNTPs RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair A tailing and sequencing adapter ligation were performed. In order to select cDNA fragments of approximately 250 300 bp samples were sonicated and magnetic beads were used to select the target fragment size post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed through size selection andPCR amplification. post cDNA library completion a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific USA followed by Agilent 2100 Bioanalyzer to test insert size and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries from each treatment and sex were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150 generating an average of 35 million pair end reads for each sample.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP383398     M3FL_1.fq.gz M3FL_2.fq.gz fastq fastq 11853885000.0 39512950.0 M3FL 1.fq.gz 0:150 1:150 A:3129583480;C:2788314875;G:2819899471;T:3116000527;N:86647 150 150     3129583480 2788314875 2819899471 3116000527 86647 SRX15874807 SRS13564513 SRA1442579 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.96636 0.96644 0.02786 0.02873 0.84954 0.84991 0.21022 0.20905 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk unknown unknown   Portugal 2022-06-24 Adult Adult Liver Liver and Biliary System
70433 70433 SRR19831100 SRX15874806 SRS13564512 SRP383398 PRJNA851939 Danio rerio breed:Wild type Transcriptome or Gene expression PRJNA851939 Other Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       CFL CFL   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:Adult|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Ctrl female Dre Ctrl female Dre Ctrl female Briefly one RNA pool of 5 livers n=1 from each treatment and sex with a minimum concentration of 40 ng/L were subjected to a quality control to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic USA; integrity and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina USA. Subsequently sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand post which a custom second strand synthesis buffer Illumina USA as well as dNTPs RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair A tailing and sequencing adapter ligation were performed. In order to select cDNA fragments of approximately 250 300 bp samples were sonicated and magnetic beads were used to select the target fragment size post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed through size selection andPCR amplification. post cDNA library completion a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific USA followed by Agilent 2100 Bioanalyzer to test insert size and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries from each treatment and sex were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150 generating an average of 35 million pair end reads for each sample.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP383398     CFL_1.fq.gz CFL_2.fq.gz fastq fastq 9192861600.0 30642872.0 CFL 1.fq.gz 0:150 1:150 A:2437547843;C:2152133867;G:2172900538;T:2430212552;N:66800 150 150     2437547843 2152133867 2172900538 2430212552 66800 SRX15874806 SRS13564512 SRA1442579 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.96501 0.96444 0.0235 0.02404 0.84987 0.84975 0.19639 0.19629 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk unknown unknown   Portugal 2022-06-24 Adult Adult Liver Liver and Biliary System
70434 70434 SRR19831101 SRX15874805 SRS13564511 SRP383398 PRJNA851939 Danio rerio breed:Wild type Transcriptome or Gene expression PRJNA851939 Other Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       M3ML M3ML   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:Adult|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 M3 male Dre M3 male Dre M3 male Briefly one RNA pool of 5 livers n=1 from each treatment and sex with a minimum concentration of 40 ng/L were subjected to a quality control to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic USA; integrity and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina USA. Subsequently sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand post which a custom second strand synthesis buffer Illumina USA as well as dNTPs RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair A tailing and sequencing adapter ligation were performed. In order to select cDNA fragments of approximately 250 300 bp samples were sonicated and magnetic beads were used to select the target fragment size post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed through size selection andPCR amplification. post cDNA library completion a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific USA followed by Agilent 2100 Bioanalyzer to test insert size and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries from each treatment and sex were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150 generating an average of 35 million pair end reads for each sample.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP383398     M3ML_1.fq.gz M3ML_2.fq.gz fastq fastq 11013803100.0 36712677.0 M3ML 1.fq.gz 0:150 1:150 A:2930761660;C:2564890668;G:2592139298;T:2925931025;N:80449 150 150     2930761660 2564890668 2592139298 2925931025 80449 SRX15874805 SRS13564511 SRA1442579 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.94357 0.94354 0.05324 0.05301 0.7778 0.77802 0.55221 0.54977 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk unknown unknown   Portugal 2022-06-24 Adult Adult Liver Liver and Biliary System
70435 70435 SRR19831102 SRX15874804 SRS13564510 SRP383398 PRJNA851939 Danio rerio breed:Wild type Transcriptome or Gene expression PRJNA851939 Other Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       CML CML   strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:Adult|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 Ctrl male Dre Ctrl male Dre Ctrl male Briefly one RNA pool of 5 livers n=1 from each treatment and sex with a minimum concentration of 40 ng/L were subjected to a quality control to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic USA; integrity and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina USA. Subsequently sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand post which a custom second strand synthesis buffer Illumina USA as well as dNTPs RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair A tailing and sequencing adapter ligation were performed. In order to select cDNA fragments of approximately 250 300 bp samples were sonicated and magnetic beads were used to select the target fragment size post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed through size selection andPCR amplification. post cDNA library completion a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific USA followed by Agilent 2100 Bioanalyzer to test insert size and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries from each treatment and sex were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150 generating an average of 35 million pair end reads for each sample.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP383398     CML_1.fq.gz CML_2.fq.gz fastq fastq 10198111200.0 33993704.0 CML 1.fq.gz 0:150 1:150 A:2734736413;C:2355820205;G:2381029396;T:2726450659;N:74527 150 150     2734736413 2355820205 2381029396 2726450659 74527 SRX15874804 SRS13564510 SRA1442579 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.94044 0.94085 0.06098 0.06137 0.71934 0.72129 0.52142 0.53876 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk unknown unknown   Portugal 2022-06-24 Adult Adult Liver Liver and Biliary System
72238 72238 SRR22378280 SRX18348799 SRS15837099 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 9 i PP H3   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP H 3 PP H 3 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_H_3_1.clean.fq.gz PP_H_3_2.clean.fq.gz fastq fastq 6050496000.0 20168320.0 PP H 3 1.clean.fq.gz 0:150 1:150 A:1609820591;C:1404035937;G:1435709208;T:1600895822;N:34442 150 150     1609820591 1404035937 1435709208 1600895822 34442 SRX18348799 SRS15837099 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95422 0.95352 0.03356 0.0333 0.81438 0.81621 0.20548 0.20832 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72239 72239 SRR22378281 SRX18348798 SRS15837098 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 8 h PP H2   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP H 2 PP H 2 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_H_2_1.clean.fq.gz PP_H_2_2.clean.fq.gz fastq fastq 6931627800.0 23105426.0 PP H 2 1.clean.fq.gz 0:150 1:150 A:1846597632;C:1607025715;G:1643520034;T:1834444241;N:40178 150 150     1846597632 1607025715 1643520034 1834444241 40178 SRX18348798 SRS15837098 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95569 0.95532 0.03341 0.03305 0.81552 0.81613 0.20708 0.20637 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72240 72240 SRR22378282 SRX18348797 SRS15837097 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 7 g PP H1   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP H 1 PP H 1 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_H_1_1.clean.fq.gz PP_H_1_2.clean.fq.gz fastq fastq 6965779200.0 23219264.0 PP H 1 1.clean.fq.gz 0:150 1:150 A:1854993351;C:1615581171;G:1652213415;T:1842951099;N:40164 150 150     1854993351 1615581171 1652213415 1842951099 40164 SRX18348797 SRS15837097 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95521 0.95346 0.0346 0.03362 0.81329 0.81397 0.21476 0.21542 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72241 72241 SRR22378283 SRX18348796 SRS15837096 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 6 f PP L3   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP L 3 PP L 3 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_L_3_1.clean.fq.gz PP_L_3_2.clean.fq.gz fastq fastq 6425772600.0 21419242.0 PP L 3 1.clean.fq.gz 0:150 1:150 A:1708813613;C:1492784511;G:1526083182;T:1698053917;N:37377 150 150     1708813613 1492784511 1526083182 1698053917 37377 SRX18348796 SRS15837096 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95255 0.9517 0.03262 0.03276 0.78932 0.79001 0.23796 0.23759 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72242 72242 SRR22378284 SRX18348795 SRS15837095 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 5 e PP L2   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP L 2 PP L 2 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_L_2_1.clean.fq.gz PP_L_2_2.clean.fq.gz fastq fastq 7364967000.0 24549890.0 PP L 2 1.clean.fq.gz 0:150 1:150 A:1957845917;C:1711368393;G:1748629219;T:1947080701;N:42770 150 150     1957845917 1711368393 1748629219 1947080701 42770 SRX18348795 SRS15837095 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95442 0.95483 0.03265 0.03247 0.78861 0.78882 0.22507 0.2264 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72243 72243 SRR22378285 SRX18348794 SRS15837094 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 4 d PP L1   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver PP L 1 PP L 1 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     PP_L_1_2.clean.fq.gz PP_L_1_1.clean.fq.gz fastq fastq 6777441600.0 22591472.0 PP L 1 1.clean.fq.gz 0:150 1:150 A:1800305520;C:1575234885;G:1609944648;T:1791917239;N:39308 150 150     1800305520 1575234885 1609944648 1791917239 39308 SRX18348794 SRS15837094 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.95591 0.9549 0.03272 0.03252 0.78932 0.78975 0.22756 0.22649 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72244 72244 SRR22378286 SRX18348793 SRS15837093 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 3 c Ctrol3   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver Ctrol 3 Ctrol 3 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     Ctrol_3_1.clean.fq.gz Ctrol_3_2.clean.fq.gz fastq fastq 6834216900.0 22780723.0 Ctrol 3 1.clean.fq.gz 0:150 1:150 A:1822326066;C:1583590643;G:1613523573;T:1814737039;N:39579 150 150     1822326066 1583590643 1613523573 1814737039 39579 SRX18348793 SRS15837093 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.94711 0.94633 0.04169 0.04124 0.78313 0.78468 0.29959 0.29801 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72245 72245 SRR22378287 SRX18348792 SRS15837092 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 2 b Ctrol2   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver Ctrol 2 Ctrol 2 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     Ctrol_2_1.clean.fq.gz Ctrol_2_2.clean.fq.gz fastq fastq 7012059300.0 23373531.0 Ctrol 2 1.clean.fq.gz 0:150 1:150 A:1871625597;C:1622333650;G:1653663999;T:1864395002;N:41052 150 150     1871625597 1622333650 1653663999 1864395002 41052 SRX18348792 SRS15837092 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.94859 0.94775 0.04252 0.04198 0.7823 0.78177 0.29534 0.29188 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72246 72246 SRR22378288 SRX18348791 SRS15837091 SRP409217 PRJNA902840 Effects of microplastics on zebrafish PRJNA902840 Other Effect of mask derived microplastics on zebrafish liver     replicate=biological replicate 1 a Ctrol1   strain:TU|age:3 mpf|sex:not collected|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptome sequencing of zebrafish liver Ctrol 1 Ctrol 1 Whole Transcriptome     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP409217     Ctrol_1_2.clean.fq.gz Ctrol_1_1.clean.fq.gz fastq fastq 7432915500.0 24776385.0 Ctrol 1 1.clean.fq.gz 0:150 1:150 A:1982293202;C:1721858347;G:1756583773;T:1972137080;N:43098 150 150     1982293202 1721858347 1756583773 1972137080 43098 SRX18348791 SRS15837091 SRA1545405 Fujian Agriculture and Forestry University|college of marine sciences Fujian Agriculture and Forestry University 2 0.94871 0.94839 0.04182 0.04126 0.78029 0.78033 0.29469 0.293 150 150 B B biological fallback assumption illumina novaseq_era full_length random_priming unknown bulk unknown unknown   China 2022-11-22 Adult Adult Liver Liver and Biliary System
72351 72351 SRR22443584 SRX18412509 SRS15895526 SRP410422 PRJNA906165 Danio rerio strain:wild type Raw sequence reads PRJNA906165 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       Female liver MET Female liver MET   strain:wild type|age:9 mpf|dev stage:adult|sex:female|tissue:Liver|BioSampleModel:Model organism or animal                 Liver MET exposed female female met liver female met liver The current study assessed the long term direct effects of environmentally relevant concentrations of MET ng/L to low g/L on parental F0 zebrafish from egg to 9 mpf     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP410422     D1_1.fq.gz D1_2.fq.gz D3_1.fq.gz D3_2.fq.gz D4_1.fq.gz D4_2.fq.gz fastq fastq fastq fastq fastq fastq 20388437100.0 67961457.0 D1 1.fq.gz 0:150 1:150 A:5354858295;C:4849401096;G:4857966731;T:5325615610;N:595368 150 150     5354858295 4849401096 4857966731 5325615610 595368 SRX18412509 SRS15895526 SRA1548910 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.96661 0.96256 0.02628 0.02594 0.86212 0.86358 0.21071 0.20689 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2022-11-29 Adult Adult Liver Liver and Biliary System
72352 72352 SRR22443585 SRX18412508 SRS15895525 SRP410422 PRJNA906165 Danio rerio strain:wild type Raw sequence reads PRJNA906165 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       Male liver MET Male liver MET   strain:wild type|age:9 mpf|dev stage:adult|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 Liver MET exposed male male met liver male met liver The current study assessed the long term direct effects of environmentally relevant concentrations of MET ng/L to low g/L on parental F0 zebrafish from egg to 9 mpf     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP410422     B1_1.fq.gz B1_2.fq.gz B2_1.fq.gz B2_2.fq.gz B3_1.fq.gz B3_2.fq.gz B4_1.fq.gz B4_2.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq 33335183100.0 111117277.0 B1 1.fq.gz 0:150 1:150 A:8830419381;C:7868342054;G:7879335887;T:8756786672;N:299106 150 150     8830419381 7868342054 7879335887 8756786672 299106 SRX18412508 SRS15895525 SRA1548910 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.94325 0.94025 0.05608 0.05535 0.77137 0.774 0.54692 0.54855 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2022-11-29 Adult Adult Liver Liver and Biliary System
72353 72353 SRR22443586 SRX18412507 SRS15895524 SRP410422 PRJNA906165 Danio rerio strain:wild type Raw sequence reads PRJNA906165 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       Female liver ctrl Female liver ctrl   strain:wild type|age:9 mpf|dev stage:adult|sex:female|tissue:Liver|BioSampleModel:Model organism or animal                 Liver control female female ctrl liver female ctrl liver The current study assessed the long term direct effects of environmentally relevant concentrations of MET ng/L to low g/L on parental F0 zebrafish from egg to 9 mpf     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP410422     C1_1.fq.gz C1_2.fq.gz C2_1.fq.gz C2_2.fq.gz C3_1.fq.gz C3_2.fq.gz fastq fastq fastq fastq fastq fastq 22323632100.0 74412107.0 C1 1.fq.gz 0:150 1:150 A:5886382633;C:5291371393;G:5298416227;T:5847032411;N:429436 150 150     5886382633 5291371393 5298416227 5847032411 429436 SRX18412507 SRS15895524 SRA1548910 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.968 0.96517 0.02862 0.02861 0.84068 0.8409 0.20917 0.20825 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2022-11-29 Adult Adult Liver Liver and Biliary System
72354 72354 SRR22443587 SRX18412506 SRS15895523 SRP410422 PRJNA906165 Danio rerio strain:wild type Raw sequence reads PRJNA906165 Whole Genome Sequencing Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected       Male liver ctrl Male liver ctrl   strain:wild type|age:9 mpf|dev stage:adult|sex:male|tissue:Liver|BioSampleModel:Model organism or animal                 Liver control male male ctrl liver male ctrl liver The current study assessed the long term direct effects of environmentally relevant concentrations of MET ng/L to low g/L on parental F0 zebrafish from egg to 9 mpf     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP410422     A2_1.fq.gz A2_2.fq.gz A3_1.fq.gz A3_2.fq.gz A4_1.fq.gz A4_2.fq.gz fastq fastq fastq fastq fastq fastq 21112496700.0 70374989.0 A2 1.fq.gz 0:150 1:150 A:5623149607;C:4955029188;G:4952782847;T:5581010467;N:524591 150 150     5623149607 4955029188 4952782847 5581010467 524591 SRX18412506 SRS15895523 SRA1548910 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina CIIMAR - Interdisciplinary Centre of Marine and Environmental Research 2 0.93889 0.93365 0.06295 0.06217 0.74773 0.75006 0.54898 0.55855 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Portugal 2022-11-29 Adult Adult Liver Liver and Biliary System

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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");;