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run_metadata

69 rows where devstage_curation_coarse = "Undetermined" and tissue_curation_coarse = "Cell Line"

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experiment.library_selection 3

technology 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Cell Line · 69 ✖

tissue_curation 1

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

  • Undetermined · 69 ✖

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
28458 28458 SRR26265233 SRX21974767 SRS19050630 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 10|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND2 IFND2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-2.R2.fq.gz IFN4-2.R1.fq.gz fastq fastq 6934783900.0 23533465.0 IFN4 2.R1.fq.gz 0:147.35 1:147.33 A:1868083790;C:1590902416;G:1598661179;T:1876555558;N:580957 147 147     1868083790 1590902416 1598661179 1876555558 580957 SRX21974767 SRS19050630 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95226 0.95256 0.09237 0.09199 0.73403 0.73472 0.50112 0.4946 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28459 28459 SRR26265234 SRX21974766 SRS19050629 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 9|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND1 IFND1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-1.R2.fq.gz IFN4-1.R1.fq.gz fastq fastq 6955503146.0 23557276.0 IFN4 1.R1.fq.gz 0:147.65 1:147.61 A:1873984869;C:1595727817;G:1603714470;T:1881209728;N:866262 147 147     1873984869 1595727817 1603714470 1881209728 866262 SRX21974766 SRS19050629 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95329 0.95472 0.09371 0.09311 0.73535 0.7362 0.49542 0.49872 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28460 28460 SRR26265235 SRX21974765 SRS19050628 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 8|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA4 IFNA4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-4.R1.fq.gz IFN1-4.R2.fq.gz fastq fastq 6497442039.0 22025966.0 IFN1 4.R1.fq.gz 0:147.50 1:147.49 A:1752434033;C:1488528327;G:1495225910;T:1760699235;N:554534 147 147     1752434033 1488528327 1495225910 1760699235 554534 SRX21974765 SRS19050628 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95168 0.95288 0.09073 0.09058 0.73691 0.73697 0.49659 0.49706 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28461 28461 SRR26265236 SRX21974764 SRS19050627 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 7|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA3 IFNA3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-3.R1.fq.gz IFN1-3.R2.fq.gz fastq fastq 6258791362.0 21164255.0 IFN1 3.R1.fq.gz 0:147.88 1:147.85 A:1687323085;C:1434335716;G:1441365307;T:1695236268;N:530986 147 147     1687323085 1434335716 1441365307 1695236268 530986 SRX21974764 SRS19050627 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95206 0.95262 0.09255 0.09194 0.73549 0.73503 0.49685 0.50433 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28462 28462 SRR26265237 SRX21974763 SRS19050626 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA2 IFNA2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-2.R1.fq.gz IFN1-2.R2.fq.gz fastq fastq 5566110483.0 18875664.0 IFN1 2.R1.fq.gz 0:147.46 1:147.43 A:1498457518;C:1278011392;G:1284254482;T:1504942516;N:444575 147 147     1498457518 1278011392 1284254482 1504942516 444575 SRX21974763 SRS19050626 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95197 0.9524 0.09035 0.08962 0.73606 0.73634 0.50146 0.49994 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28463 28463 SRR26265238 SRX21974762 SRS19050625 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA1 IFNA1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-1.R1.fq.gz IFN1-1.R2.fq.gz fastq fastq 6919610192.0 23425305.0 IFN1 1.R1.fq.gz 0:147.71 1:147.68 A:1863998722;C:1587286271;G:1595557648;T:1872190552;N:576999 147 147     1863998722 1587286271 1595557648 1872190552 576999 SRX21974762 SRS19050625 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95297 0.95392 0.08926 0.0886 0.73744 0.73716 0.48737 0.49536 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28464 28464 SRR26265239 SRX21974761 SRS19050624 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C4 C4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-4.R1.fq.gz Control-4.R2.fq.gz fastq fastq 7048754711.0 23843338.0 Control 4.R1.fq.gz 0:147.83 1:147.80 A:1886695953;C:1629137936;G:1637672845;T:1894536437;N:711540 147 147     1886695953 1629137936 1637672845 1894536437 711540 SRX21974761 SRS19050624 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.9556 0.95723 0.09014 0.08984 0.73533 0.73643 0.50146 0.50134 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28465 28465 SRR26265240 SRX21974760 SRS19050623 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C3 C3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-3.R1.fq.gz Control-3.R2.fq.gz fastq fastq 6936430397.0 23495179.0 Control 3.R1.fq.gz 0:147.63 1:147.60 A:1861679698;C:1598594022;G:1606747561;T:1868699697;N:709419 147 147     1861679698 1598594022 1606747561 1868699697 709419 SRX21974760 SRS19050623 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95496 0.95472 0.09092 0.08958 0.73505 0.73586 0.50541 0.50256 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28466 28466 SRR26265241 SRX21974759 SRS19050622 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 12|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND4 IFND4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-4.R1.fq.gz IFN4-4.R2.fq.gz fastq fastq 6904025687.0 23391394.0 IFN4 4.R1.fq.gz 0:147.59 1:147.56 A:1858866141;C:1585020535;G:1592940944;T:1866550686;N:647381 147 147     1858866141 1585020535 1592940944 1866550686 647381 SRX21974759 SRS19050622 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95345 0.95394 0.08901 0.08834 0.73537 0.73596 0.50012 0.49674 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28467 28467 SRR26265242 SRX21974758 SRS19050621 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 11|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND3 IFND3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-3.R1.fq.gz IFN4-3.R2.fq.gz fastq fastq 6983243474.0 23627912.0 IFN4 3.R1.fq.gz 0:147.80 1:147.75 A:1880838380;C:1603492441;G:1611871993;T:1885974103;N:1066557 147 147     1880838380 1603492441 1611871993 1885974103 1066557 SRX21974758 SRS19050621 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95262 0.95399 0.09442 0.09269 0.73586 0.73519 0.50113 0.49912 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28468 28468 SRR26265243 SRX21974757 SRS19050620 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C2 C2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-2.R1.fq.gz Control-2.R2.fq.gz fastq fastq 7064416471.0 23901145.0 Control 2.R1.fq.gz 0:147.80 1:147.77 A:1896430007;C:1626943513;G:1635235356;T:1905174563;N:633032 147 147     1896430007 1626943513 1635235356 1905174563 633032 SRX21974757 SRS19050620 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95546 0.95678 0.08984 0.08994 0.73535 0.73565 0.49891 0.49705 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28469 28469 SRR26265244 SRX21974756 SRS19050619 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C1 C1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-1.R1.fq.gz Control-1.R2.fq.gz fastq fastq 7005585889.0 23733330.0 Control 1.R1.fq.gz 0:147.61 1:147.57 A:1874251473;C:1620035540;G:1628125464;T:1882607735;N:565677 147 147     1874251473 1620035540 1628125464 1882607735 565677 SRX21974756 SRS19050619 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95539 0.95612 0.08699 0.08663 0.73777 0.73833 0.49693 0.49816 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28470 28470 SRR26253203 SRX21963295 SRS19039869 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN4 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 22|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFND2 Small RNA IFND2 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN4-2.deadaptor.fq.gz fastq 278362309.0 11056139.0 IFN4 2.deadaptor.fq.gz 0:25.18 A:71944968;C:54562141;G:73333701;T:78511075;N:10424 25       71944968 54562141 73333701 78511075 10424 SRX21963295 SRS19039869 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.93133   0.07401   0.96181   0.74558   31   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28471 28471 SRR26253204 SRX21963294 SRS19039868 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN4 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 21|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFND1 Small RNA IFND1 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN4-1.deadaptor.fq.gz fastq 289362334.0 11048590.0 IFN4 1.deadaptor.fq.gz 0:26.19 A:73933649;C:59386039;G:76847534;T:79184583;N:10529 26       73933649 59386039 76847534 79184583 10529 SRX21963294 SRS19039868 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.91683   0.07099   0.96132   0.64882   25   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28472 28472 SRR26253205 SRX21963293 SRS19039867 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN1 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 20|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFNA4 Small RNA IFNA4 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN1-4.deadaptor.fq.gz fastq 270529395.0 11070360.0 IFN1 4.deadaptor.fq.gz 0:24.44 A:69759888;C:54924667;G:71358091;T:74470720;N:16029 24       69759888 54924667 71358091 74470720 16029 SRX21963293 SRS19039867 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.88469   0.06696   0.96664   0.74853   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28473 28473 SRR26253206 SRX21963292 SRS19039866 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN1 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 19|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFNA3 Small RNA IFNA3 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN1-3.deadaptor.fq.gz fastq 353291957.0 11740560.0 IFN1 3.deadaptor.fq.gz 0:30.09 A:89026549;C:76490337;G:94719420;T:93036955;N:18696 30       89026549 76490337 94719420 93036955 18696 SRX21963292 SRS19039866 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.83151   0.07199   0.96471   0.71641   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28474 28474 SRR26253207 SRX21963291 SRS19039865 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN1 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 18|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFNA2 Small RNA IFNA2 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN1-2.deadaptor.fq.gz fastq 257949577.0 11213774.0 IFN1 2.deadaptor.fq.gz 0:23.00 A:67371681;C:51128621;G:67605590;T:71826657;N:17028 23       67371681 51128621 67605590 71826657 17028 SRX21963291 SRS19039865 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.91396   0.06536   0.97197   0.76269   23   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28475 28475 SRR26253208 SRX21963290 SRS19039864 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN1 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 17|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFNA1 Small RNA IFNA1 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN1-1.deadaptor.fq.gz fastq 329358383.0 11799176.0 IFN1 1.deadaptor.fq.gz 0:27.91 A:84093681;C:68961271;G:86502739;T:89779605;N:21087 27       84093681 68961271 86502739 89779605 21087 SRX21963290 SRS19039864 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.92116   0.07483   0.96796   0.75179   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28476 28476 SRR26253209 SRX21963289 SRS19039863 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA Control 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 16|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA C4 Small RNA C4 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     Control-4.deadaptor.fq.gz fastq 251577736.0 10951659.0 Control 4.deadaptor.fq.gz 0:22.97 A:65382449;C:50041232;G:66038625;T:70106464;N:8966 22       65382449 50041232 66038625 70106464 8966 SRX21963289 SRS19039863 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.89744   0.06821   0.96607   0.63829   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28477 28477 SRR26253210 SRX21963288 SRS19039862 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA Control 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 15|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA C3 Small RNA C3 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     Control-3.deadaptor.fq.gz fastq 252164979.0 11004167.0 Control 3.deadaptor.fq.gz 0:22.92 A:65850899;C:48466665;G:66708038;T:71130786;N:8591 22       65850899 48466665 66708038 71130786 8591 SRX21963288 SRS19039862 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.91567   0.06804   0.96278   0.75579   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28478 28478 SRR26253211 SRX21963287 SRS19039861 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN4 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 24|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFND4 Small RNA IFND4 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN4-4.deadaptor.fq.gz fastq 291708053.0 11503883.0 IFN4 4.deadaptor.fq.gz 0:25.36 A:74079231;C:61368459;G:76898572;T:79351225;N:10566 25       74079231 61368459 76898572 79351225 10566 SRX21963287 SRS19039861 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.88888   0.0633   0.97305   0.74862   23   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28479 28479 SRR26253212 SRX21963286 SRS19039860 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA IFN4 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 23|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA IFND3 Small RNA IFND3 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     IFN4-3.deadaptor.fq.gz fastq 349995495.0 11885662.0 IFN4 3.deadaptor.fq.gz 0:29.45 A:87443709;C:76373108;G:92741296;T:93425866;N:11516 29       87443709 76373108 92741296 93425866 11516 SRX21963286 SRS19039860 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.92619   0.06843   0.9709   0.74977   73   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28480 28480 SRR26253213 SRX21963285 SRS19039859 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA Control 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 14|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA C2 Small RNA C2 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     Control-2.deadaptor.fq.gz fastq 254163676.0 10744164.0 Control 2.deadaptor.fq.gz 0:23.66 A:66003417;C:49309846;G:67463940;T:71377644;N:8829 23       66003417 49309846 67463940 71377644 8829 SRX21963285 SRS19039859 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.93068   0.06626   0.96441   0.7492   22   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
28481 28481 SRR26253214 SRX21963284 SRS19039858 SRP464138 PRJNA1022587 Danio rerio Raw sequence reads PRJNA1022587 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.         Small RNA Control 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 13|BioSampleModel:Model organism or animal                 Small RNAseq of zebrafish Small RNA C1 Small RNA C1 small RNA seq of zebrafish     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP464138     Control-1.deadaptor.fq.gz fastq 267090429.0 11027241.0 Control 1.deadaptor.fq.gz 0:24.22 A:70162511;C:50705437;G:69872659;T:76339682;N:10140 24       70162511 50705437 69872659 76339682 10140 SRX21963284 SRS19039858 SRA1724093 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 1 0.93267   0.07189   0.96735   0.75447   21   B   usable mapping rate illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-10-02 Undetermined Undetermined Cell Line Cell Line
49815 49815 SRR8987978 SRX5767074 SRS4701368 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       24h 6 sample exposed to microcystin for xxxh replicate #6   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #6|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #6 24h 3 24h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h3_clean_R2.fq.gz 24h3_clean_R1.fq.gz fastq fastq 6275458528.0 20779664.0 24h3 clean R1.fq.gz 0:151 1:151 A:1685303886;C:1437291030;G:1447147160;T:1702856463;N:2859989 151 151     1685303886 1437291030 1447147160 1702856463 2859989 SRX5767074 SRS4701368 SRA880742 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92675 0.92679 0.13415 0.13431 0.73945 0.74213 0.50477 0.50726 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49816 49816 SRR8987979 SRX5767073 SRS4701367 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       24h 4 sample exposed to microcystin for xxxh replicate #4   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #4|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #4 24h 1 24h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h1_clean_R1.fq.gz 24h1_clean_R2.fq.gz fastq fastq 6373552356.0 21104478.0 24h1 clean R1.fq.gz 0:151 1:151 A:1712827186;C:1458408871;G:1470508604;T:1728973011;N:2834684 151 151     1712827186 1458408871 1470508604 1728973011 2834684 SRX5767073 SRS4701367 SRA880742 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9248 0.92582 0.13207 0.13239 0.73839 0.74038 0.49865 0.50119 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49817 49817 SRR8987980 SRX5767072 SRS4701366 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       24h 5 sample exposed to microcystin for xxxh replicate #5   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #5|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #5 24h 2 24h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h2_clean_R2.fq.gz 24h2_clean_R1.fq.gz fastq fastq 6303822066.0 20873583.0 24h2 clean R1.fq.gz 0:151 1:151 A:1694366688;C:1441733171;G:1453717629;T:1711017538;N:2987040 151 151     1694366688 1441733171 1453717629 1711017538 2987040 SRX5767072 SRS4701366 SRA880742 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9264 0.92591 0.13121 0.13204 0.7385 0.74227 0.50323 0.49357 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49818 49818 SRR8983315 SRX5762615 SRS4697269 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       12h 5 sample exposed to microcystin for xxxh replicate #5   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #5|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #5 12h 5 12h 5 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h2_clean_R1.fq.gz 12h2_clean_R2.fq.gz fastq fastq 5637564766.0 18667433.0 12h2 clean R1.fq.gz 0:151 1:151 A:1484457309;C:1319928521;G:1331480348;T:1498547286;N:3151302 151 151     1484457309 1319928521 1331480348 1498547286 3151302 SRX5762615 SRS4697269 SRA880316 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93974 0.93913 0.09518 0.09588 0.74982 0.75331 0.49858 0.49712 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49819 49819 SRR8983316 SRX5762614 SRS4697268 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       12h 4 sample exposed to microcystin for xxxh replicate #4   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #4|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #4 12h 4 12h 4 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h1_clean_R2.fq.gz 12h1_clean_R1.fq.gz fastq fastq 5742037438.0 19013369.0 12h1 clean R1.fq.gz 0:151 1:151 A:1505967171;C:1350499061;G:1361100937;T:1521258216;N:3212053 151 151     1505967171 1350499061 1361100937 1521258216 3212053 SRX5762614 SRS4697268 SRA880316 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9408 0.93974 0.09145 0.09155 0.75146 0.75501 0.49821 0.49267 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49820 49820 SRR8983317 SRX5762613 SRS4697267 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       12h 6 sample exposed to microcystin for xxxh replicate #6   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #6|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #6 12h 6 12h 6 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h3_clean_R2.fq.gz 12h3_clean_R1.fq.gz fastq fastq 5456135246.0 18066673.0 12h3 clean R1.fq.gz 0:151 1:151 A:1445780220;C:1268483624;G:1278423072;T:1460394475;N:3053855 151 151     1445780220 1268483624 1278423072 1460394475 3053855 SRX5762613 SRS4697267 SRA880316 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93632 0.93624 0.10093 0.1015 0.7499 0.75367 0.50485 0.50164 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49821 49821 SRR8982954 SRX5762254 SRS4696966 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       6h 6 sample exposed to microcystin for xxxh replicate #6   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #6|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #6 6h 6 6h 6 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h3_clean_R1.fq.gz 6h3_clean_R2.fq.gz fastq fastq 7939056332.0 26288266.0 6h3 clean R1.fq.gz 0:151 1:151 A:2043932346;C:1908038526;G:1925388013;T:2058202469;N:3494978 151 151     2043932346 1908038526 1925388013 2058202469 3494978 SRX5762254 SRS4696966 SRA880287 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.94661 0.94661 0.07559 0.07638 0.76134 0.76394 0.49736 0.50336 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49822 49822 SRR8982955 SRX5762253 SRS4696965 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       6h 5 sample exposed to microcystin for xxxh replicate #5   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #5|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #5 6h 5 6h 5 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h2_clean_R1.fq.gz 6h2_clean_R2.fq.gz fastq fastq 5431283968.0 17984384.0 6h2 clean R1.fq.gz 0:151 1:151 A:1432960105;C:1269588003;G:1284040697;T:1441657813;N:3037350 151 151     1432960105 1269588003 1284040697 1441657813 3037350 SRX5762253 SRS4696965 SRA880287 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9325 0.93223 0.11537 0.11461 0.7433 0.7457 0.49688 0.50558 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49823 49823 SRR8982956 SRX5762252 SRS4696964 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       6h 4 sample exposed to microcystin for xxxh replicate #4   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #4|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #4 6h 4 6h 4 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h1_clean_R1.fq.gz 6h1_clean_R2.fq.gz fastq fastq 5561923128.0 18416964.0 6h1 clean R1.fq.gz 0:151 1:151 A:1439698401;C:1327963901;G:1340151064;T:1450995064;N:3114698 151 151     1439698401 1327963901 1340151064 1450995064 3114698 SRX5762252 SRS4696964 SRA880287 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9438 0.94314 0.08661 0.08624 0.75613 0.75858 0.49468 0.47945 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-29 Undetermined Undetermined Cell Line Cell Line
49824 49824 SRR8981191 SRX5760491 SRS4695477 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       3h 5 sample exposed to microcystin for xxxh replicate #5   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #5|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #5 3h 5 3h 5 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h2_clean_R1.fq.gz 3h2_clean_R2.fq.gz fastq fastq 5426694474.0 17969187.0 3h2 clean R1.fq.gz 0:151 1:151 A:1455679038;C:1243463586;G:1253806438;T:1470703342;N:3042070 151 151     1455679038 1243463586 1253806438 1470703342 3042070 SRX5760491 SRS4695477 SRA880231 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92775 0.9265 0.13003 0.13039 0.74257 0.74679 0.48728 0.50236 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-28 Undetermined Undetermined Cell Line Cell Line
49825 49825 SRR8981192 SRX5760490 SRS4695476 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       3h 4 sample exposed to microcystin for xxxh replicate #4   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #4|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #4 3h 4 3h 4 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h1_clean_R1.fq.gz 3h1_clean_R2.fq.gz fastq fastq 6381408584.0 21130492.0 3h1 clean R1.fq.gz 0:151 1:151 A:1704493392;C:1471437290;G:1482728107;T:1720014953;N:2734842 151 151     1704493392 1471437290 1482728107 1720014953 2734842 SRX5760490 SRS4695476 SRA880231 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93 0.93014 0.11977 0.12069 0.74434 0.74864 0.49627 0.50428 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-28 Undetermined Undetermined Cell Line Cell Line
49826 49826 SRR8981193 SRX5760489 SRS4695475 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       3h 6 sample exposed to microcystin for xxxh replicate #6   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #6|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #6 3h 6 3h 6 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h3_clean_R1.fq.gz 3h3_clean_R2.fq.gz fastq fastq 6058080740.0 20059870.0 3h3 clean R1.fq.gz 0:151 1:151 A:1623401423;C:1391994584;G:1400166489;T:1639132542;N:3385702 151 151     1623401423 1391994584 1400166489 1639132542 3385702 SRX5760489 SRS4695475 SRA880231 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93298 0.93201 0.10907 0.10885 0.75059 0.75463 0.50656 0.49273 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-28 Undetermined Undetermined Cell Line Cell Line
49827 49827 SRR8961086 SRX5740640 SRS4676161 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       1h 6 sample exposed to microcystin for xxxh replicate #6   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #6|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #6 1h 6 1h 6 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h3_clean_R1.fq.gz 1h3_clean_R2.fq.gz fastq fastq 6472187368.0 21431084.0 1h3 clean R1.fq.gz 0:151 1:151 A:1780621052;C:1438221849;G:1453983421;T:1796459482;N:2901564 151 151     1780621052 1438221849 1453983421 1796459482 2901564 SRX5740640 SRS4676161 SRA879791 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92158 0.91814 0.14503 0.14358 0.75775 0.75982 0.50094 0.49955 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49828 49828 SRR8961087 SRX5740639 SRS4676160 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       1h 4 sample exposed to microcystin for xxxh replicate #4   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #4|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #4 1h 4 1h 4 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h1_clean_R1.fq.gz 1h1_clean_R2.fq.gz fastq fastq 6177620796.0 20455698.0 1h1 clean R1.fq.gz 0:151 1:151 A:1646973061;C:1422549043;G:1441385824;T:1663912518;N:2800350 151 151     1646973061 1422549043 1441385824 1663912518 2800350 SRX5740639 SRS4676160 SRA879791 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93085 0.92866 0.12633 0.12579 0.75812 0.76136 0.48992 0.50959 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49829 49829 SRR8961088 SRX5740638 SRS4676159 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       1h 5 sample exposed to microcystin for xxxh replicate #5   ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|cell line:ZFL cell line|treatment:sample exposed to microcystin for xxxh replicate #5|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxxh replicate #5 1h 5 1h 5 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h2_clean_R2.fq.gz 1h2_clean_R1.fq.gz fastq fastq 5616651266.0 18598183.0 1h2 clean R1.fq.gz 0:151 1:151 A:1492544948;C:1296049637;G:1317613246;T:1507292547;N:3150888 151 151     1492544948 1296049637 1317613246 1507292547 3150888 SRX5740638 SRS4676159 SRA879791 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93168 0.93082 0.12771 0.12751 0.75653 0.75964 0.508 0.51051 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49830 49830 SRR8959882 SRX5739436 SRS4675912 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       control replicate #6 ck 6   replicate:replicate=#6|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal                 replicate 6 ck 6 ck 6 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     CK3_clean_R1.fq.gz CK3_clean_R2.fq.gz fastq fastq 6417346282.0 21249491.0 CK3 clean R1.fq.gz 0:151 1:151 A:1753073270;C:1445910840;G:1452693305;T:1762084157;N:3584710 151 151     1753073270 1445910840 1452693305 1762084157 3584710 SRX5739436 SRS4675912 SRA879767 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92653 0.92662 0.11696 0.11682 0.75166 0.75379 0.50678 0.50594 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49831 49831 SRR8959883 SRX5739435 SRS4675911 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       control replicate #4 ck 4   replicate:replicate=#4|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal                 replicate 4 ck 4 ck 4 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     CK1_clean_R1.fq.gz CK1_clean_R2.fq.gz fastq fastq 5659831830.0 18741165.0 CK1 clean R1.fq.gz 0:151 1:151 A:1532952307;C:1289729700;G:1295220307;T:1538761250;N:3168266 151 151     1532952307 1289729700 1295220307 1538761250 3168266 SRX5739435 SRS4675911 SRA879767 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92518 0.92535 0.11332 0.11378 0.74919 0.75235 0.50223 0.49803 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49832 49832 SRR8959884 SRX5739434 SRS4675910 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       control replicate #5 ck 5   replicate:replicate=#5|ecotype:not applicable|dev stage:not applicable|sex:not applicable|tissue:ZFL cell line|BioSampleModel:Model organism or animal                 replicate 5 ck 5 ck 5 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     CK2_clean_R1.fq.gz CK2_clean_R2.fq.gz fastq fastq 5880727616.0 19472608.0 CK2 clean R1.fq.gz 0:151 1:151 A:1575999691;C:1352057289;G:1366253556;T:1583120335;N:3296745 151 151     1575999691 1352057289 1366253556 1583120335 3296745 SRX5739434 SRS4675910 SRA879767 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93653 0.9349 0.09037 0.09026 0.76262 0.76572 0.51143 0.50376 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-04-26 Undetermined Undetermined Cell Line Cell Line
49833 49833 SRR8133154 SRX4954244 SRS3995636 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #1 24h 1   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #1|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #1 24h 1 24h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h-1_R1.fastq.gz 24h-1_R2.fastq.gz fastq fastq 6408674352.0 21220776.0 24h 1 R1.fastq.gz 0:151 1:151 A:1752104547;C:1447174976;G:1451968217;T:1757298923;N:127689 151 151     1752104547 1447174976 1451968217 1757298923 127689 SRX4954244 SRS3995636 SRA800477 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9212 0.91969 0.14419 0.14446 0.73677 0.74363 0.49228 0.49725 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-30 Undetermined Undetermined Cell Line Cell Line
49834 49834 SRR8133155 SRX4954243 SRS3995635 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #2 24h 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #2|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #2 24h 2 24h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h-2_R1.fastq.gz 24h-2_R2.fastq.gz fastq fastq 6331528754.0 20965327.0 24h 2 R1.fastq.gz 0:151 1:151 A:1725083256;C:1436372645;G:1442486884;T:1727457912;N:128057 151 151     1725083256 1436372645 1442486884 1727457912 128057 SRX4954243 SRS3995635 SRA800477 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92281 0.92303 0.13905 0.14045 0.73708 0.74401 0.50843 0.50295 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49835 49835 SRR8133156 SRX4954242 SRS3995634 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #3 24h 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #3|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #3 24h 3 24h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     24h-3_R1.fastq.gz 24h-3_R2.fastq.gz fastq fastq 6723114940.0 22261970.0 24h 3 R1.fastq.gz 0:151 1:151 A:1833689339;C:1522824611;G:1529534136;T:1836931192;N:135662 151 151     1833689339 1522824611 1529534136 1836931192 135662 SRX4954242 SRS3995634 SRA800477 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.91356 0.91347 0.13955 0.14059 0.73898 0.74399 0.49776 0.50087 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49836 49836 SRR8133151 SRX4954241 SRS3995633 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #3 12h 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #3|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #3 12h 3 12h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h-3_R1.fastq.gz 12h-3_R2.fastq.gz fastq fastq 6249709404.0 20694402.0 12h 3 R1.fastq.gz 0:151 1:151 A:1679876276;C:1439210018;G:1449953029;T:1680544537;N:125544 151 151     1679876276 1439210018 1449953029 1680544537 125544 SRX4954241 SRS3995633 SRA800476 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9318 0.93185 0.10315 0.10397 0.7499 0.75513 0.49669 0.50516 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49837 49837 SRR8133152 SRX4954240 SRS3995632 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #1 12h 1   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #1|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #1 12h 1 12h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h-1_R1.fastq.gz 12h-1_R2.fastq.gz fastq fastq 6040713928.0 20002364.0 12h 1 R1.fastq.gz 0:151 1:151 A:1604304459;C:1407301760;G:1430569355;T:1597934265;N:604089 151 151     1604304459 1407301760 1430569355 1597934265 604089 SRX4954240 SRS3995632 SRA800476 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93665 0.93821 0.09301 0.0957 0.75284 0.77169 0.49115 0.48606 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49838 49838 SRR8133153 SRX4954239 SRS3995631 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #2 12h 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #2|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #2 12h 2 12h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     12h-2_R1.fastq.gz 12h-2_R2.fastq.gz fastq fastq 6340973200.0 20996600.0 12h 2 R1.fastq.gz 0:151 1:151 A:1704338617;C:1461869913;G:1470728810;T:1703906206;N:129654 151 151     1704338617 1461869913 1470728810 1703906206 129654 SRX4954239 SRS3995631 SRA800476 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93272 0.93343 0.10216 0.10338 0.74978 0.75513 0.50094 0.51045 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49839 49839 SRR8132757 SRX4953863 SRS3995402 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #3 6h 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #3|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #3 6h 3 6h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h-3_R1.fastq.gz 6h-3_R2.fastq.gz fastq fastq 6533368340.0 21633670.0 6h 3 R1.fastq.gz 0:151 1:151 A:1684379253;C:1575728468;G:1593737205;T:1678875387;N:648027 151 151     1684379253 1575728468 1593737205 1678875387 648027 SRX4953863 SRS3995402 SRA800451 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.94744 0.94959 0.06681 0.06774 0.76459 0.77711 0.4873 0.49779 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49840 49840 SRR8132756 SRX4953862 SRS3995403 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #1 6h 1   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #1|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #1 6h 1 6h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h-1_R1.fastq.gz 6h-1_R2.fastq.gz fastq fastq 6686156482.0 22139591.0 6h 1 R1.fastq.gz 0:151 1:151 A:1712757343;C:1622803789;G:1646819107;T:1703094369;N:681874 151 151     1712757343 1622803789 1646819107 1703094369 681874 SRX4953862 SRS3995403 SRA800449 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.95018 0.95234 0.0661 0.06774 0.77268 0.78652 0.49287 0.48663 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-29 Undetermined Undetermined Cell Line Cell Line
49841 49841 SRR8132755 SRX4953861 SRS3995401 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #2 6h 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #2|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #2 6h 2 6h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     6h-2_R1.fastq.gz 6h-2_R2.fastq.gz fastq fastq 5551304204.0 18381802.0 6h 2 R1.fastq.gz 0:151 1:151 A:1408740987;C:1361721973;G:1380328727;T:1399965481;N:547036 151 151     1408740987 1361721973 1380328727 1399965481 547036 SRX4953861 SRS3995401 SRA800450 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.9506 0.95313 0.07031 0.07155 0.7739 0.78591 0.50125 0.49851 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-29 Undetermined Undetermined Cell Line Cell Line
49842 49842 SRR8119911 SRX4946208 SRS3988532 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #3 3h 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #3|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #3 3h 3 3h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h-3_R1.fastq.gz 3h-3_R2.fastq.gz fastq fastq 6249422202.0 20693451.0 3h 3 R1.fastq.gz 0:151 1:151 A:1700610088;C:1416827975;G:1436930329;T:1694433965;N:619845 151 151     1700610088 1416827975 1436930329 1694433965 619845 SRX4946208 SRS3988532 SRA799983 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.924 0.92633 0.13412 0.13864 0.74158 0.76489 0.49551 0.49903 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-29 Undetermined Undetermined Cell Line Cell Line
49843 49843 SRR8119910 SRX4946207 SRS3988531 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #2 3h 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #2|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #2 3h 2 3h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h-2_R1.fastq.gz 3h-2_R2.fastq.gz fastq fastq 6691460508.0 22157154.0 3h 2 R2.fastq.gz 0:151 1:151 A:1817827404;C:1520902100;G:1534921644;T:1817122657;N:686703 151 151     1817827404 1520902100 1534921644 1817122657 686703 SRX4946207 SRS3988531 SRA799982 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92541 0.92734 0.13003 0.1321 0.7443 0.76019 0.50143 0.4998 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49844 49844 SRR8117643 SRX4943940 SRS3986328 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #1 3h 1   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #1|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #1 3h 1 3h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     3h-1_R1.fastq.gz 3h-1_R2.fastq.gz fastq fastq 6151798890.0 20370195.0 3h 1 R1.fastq.gz 0:151 1:151 A:1649142984;C:1419068750;G:1435991843;T:1646989815;N:605498 151 151     1649142984 1419068750 1435991843 1646989815 605498 SRX4943940 SRS3986328 SRA799824 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92965 0.93287 0.12221 0.12677 0.73397 0.75278 0.50535 0.50378 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-28 Undetermined Undetermined Cell Line Cell Line
49845 49845 SRR8115441 SRX4941738 SRS3985539 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #3 1h 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #3|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #3 1h 3 1h 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h-3_R2.fastq.gz 1h-3_R1.fastq.gz fastq fastq 7655572254.0 25349577.0 1h 3 R2.fastq.gz 0:151 1:151 A:2078212614;C:1742053699;G:1754520045;T:2080018836;N:767060 151 151     2078212614 1742053699 1754520045 2080018836 767060 SRX4941738 SRS3985539 SRA799651 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92526 0.92744 0.12977 0.13298 0.75743 0.77061 0.50353 0.50471 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49846 49846 SRR8115440 SRX4941737 SRS3985538 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #2 1h 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #2|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #2 1h 2 1h 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h-2_R1.fastq.gz 1h-2_R2.fastq.gz fastq fastq 7594153306.0 25146203.0 1h 2 R1.fastq.gz 0:151 1:151 A:2048228795;C:1739666332;G:1763496812;T:2041988124;N:773243 151 151     2048228795 1739666332 1763496812 2041988124 773243 SRX4941737 SRS3985538 SRA799650 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92922 0.93046 0.12988 0.1333 0.75657 0.77684 0.50439 0.49684 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
49847 49847 SRR8109598 SRX4936168 SRS3980334 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample exposed to microcystin for xxx hour replicate #1 1h 1   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:exposed to microcystin for xxx hour replicate #1|BioSampleModel:Model organism or animal                 sample exposed to microcystin for xxx hour replicate #1 1h 1 1h 1 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     1h-1_R1.fastq.gz 1h-1_R2.fastq.gz fastq fastq 6505465654.0 21541277.0 1h 1 R2.fastq.gz 0:151 1:151 A:1772064909;C:1473729340;G:1487273483;T:1771747419;N:650503 151 151     1772064909 1473729340 1487273483 1771747419 650503 SRX4936168 SRS3980334 SRA798650 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.92342 0.92707 0.13549 0.13873 0.7555 0.77106 0.49839 0.50202 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-25 Undetermined Undetermined Cell Line Cell Line
49848 49848 SRR8109308 SRX4935890 SRS3980091 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample not treated replicate #3 ck 3   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:not treated replicate #3|BioSampleModel:Model organism or animal                 sample not treated replicate #3 ck 3 ck 3 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     CK-3_R1.fastq.gz CK-3_R2.fastq.gz fastq fastq 6691086632.0 22155916.0 CK 3 R2.fastq.gz 0:151 1:151 A:1817102254;C:1525946318;G:1537285128;T:1810073033;N:679899 151 151     1817102254 1525946318 1537285128 1810073033 679899 SRX4935890 SRS3980091 SRA798632 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93213 0.93388 0.10099 0.10342 0.75828 0.77035 0.49928 0.49506 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2018-10-25 Undetermined Undetermined Cell Line Cell Line
49849 49849 SRR8109041 SRX4935630 SRS3979958 SRP166817 PRJNA498018 Danio rerio strain:ZFL cell line Genome sequencing PRJNA498018 Whole Genome Sequencing Transcriptional responses of ZFL exposed to microcystin LR       sample not treated replicate #2 ck 2   isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:not treated replicate #1|BioSampleModel:Model organism or animal                 sample not treated replicate #2 ck 2 ck 2 Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP166817     CK-2_R2.fastq.gz CK-2_R1.fastq.gz fastq fastq 6135368580.0 20315790.0 CK 2 R2.fastq.gz 0:151 1:151 A:1659190299;C:1402338038;G:1422425283;T:1650808795;N:606165 151 151     1659190299 1402338038 1422425283 1650808795 606165 SRX4935630 SRS3979958 SRA798622 Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences 2 0.93276 0.93529 0.09768 0.1008 0.75905 0.77512 0.48616 0.50755 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   China 2019-01-01 Undetermined Undetermined Cell Line Cell Line
64985 64985 SRR14867731 SRX11185279 SRS9242606 SRP324746 PRJNA739457 Investigation of mettl4 mediated alterative splicing variation GSE178511 Other We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT       ZEBARFISH WT AB9 Sample 23 GSM5393117   tissue:ZEBARFISH|genotype:WT|cell line:AB9 ZEBARFISH WT AB9  Sample 23 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10 dm6 sacCer1 GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample ZEBARFISH   RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype:WT|cell line:AB9 GSM5393117 GSM5393117: ZEBARFISH WT AB9 Sample 23; Danio rerio; RNA Seq GSM5393117   1 RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5393117 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP324746     ZEBRAFISH-WT-1_R1_001.fastq.gz ZEBRAFISH-WT-1_R2_001.fastq.gz fastq fastq 8653301400.0 28844338.0 GSM5393117 r1 0:150 1:150 A:2002938965;C:2340373383;G:2308705634;T:2000755068;N:528350 150 150     2002938965 2340373383 2308705634 2000755068 528350 SRX11185279 SRS9242606 SRA1248203 GEO Max Planck Institute for heart and lung research 2 0.03799 0.045 0.00894 0.00762 0.99744 0.99754 0.58095 0.65007 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Germany 2021-06-20 Undetermined Undetermined Cell Line Cell Line
64986 64986 SRR14867730 SRX11185278 SRS9242605 SRP324746 PRJNA739457 Investigation of mettl4 mediated alterative splicing variation GSE178511 Other We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT       ZEBARFISH KO AB9 Sample 22 GSM5393116   tissue:ZEBARFISH|genotype:KO|cell line:AB9 ZEBARFISH KO AB9  Sample 22 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10 dm6 sacCer1 GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample ZEBARFISH   RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype:KO|cell line:AB9 GSM5393116 GSM5393116: ZEBARFISH KO AB9 Sample 22; Danio rerio; RNA Seq GSM5393116   1 RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5393116 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP324746     ZEBRAFISH-KO-1_R1_001.fastq.gz ZEBRAFISH-KO-1_R2_001.fastq.gz fastq fastq 9207894900.0 30692983.0 GSM5393116 r1 0:150 1:150 A:2082839316;C:2538526142;G:2516073664;T:2069867517;N:588261 150 150     2082839316 2538526142 2516073664 2069867517 588261 SRX11185278 SRS9242605 SRA1248203 GEO Max Planck Institute for heart and lung research 2 0.0438 0.05067 0.00926 0.00821 0.99811 0.99809 0.5419 0.60225 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Germany 2021-06-20 Undetermined Undetermined Cell Line Cell Line
64987 64987 SRR14867729 SRX11185277 SRS9242604 SRP324746 PRJNA739457 Investigation of mettl4 mediated alterative splicing variation GSE178511 Other We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT       ZEBARFISH WT AB9 Sample 21 GSM5393115   tissue:ZEBARFISH|genotype:WT|cell line:AB9 ZEBARFISH WT AB9  Sample 21 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10 dm6 sacCer1 GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample ZEBARFISH   RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype:WT|cell line:AB9 GSM5393115 GSM5393115: ZEBARFISH WT AB9 Sample 21; Danio rerio; RNA Seq GSM5393115   1 RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5393115 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP324746     ZEBARFISH-WT-2_R1_001.fastq.gz ZEBARFISH-WT-2_R2_001.fastq.gz fastq fastq 10653778500.0 35512595.0 GSM5393115 r1 0:150 1:150 A:2472673652;C:2874537502;G:2838089387;T:2467827251;N:650708 150 150     2472673652 2874537502 2838089387 2467827251 650708 SRX11185277 SRS9242604 SRA1248203 GEO Max Planck Institute for heart and lung research 2 0.03862 0.04475 0.0091 0.00761 0.99799 0.99797 0.57868 0.65107 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Germany 2021-06-20 Undetermined Undetermined Cell Line Cell Line
64988 64988 SRR14867728 SRX11185276 SRS9242603 SRP324746 PRJNA739457 Investigation of mettl4 mediated alterative splicing variation GSE178511 Other We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT       ZEBARFISH KO AB9 Sample 20 GSM5393114   tissue:ZEBARFISH|genotype:KO|cell line:AB9 ZEBARFISH KO AB9  Sample 20 Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10 dm6 sacCer1 GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample ZEBARFISH   RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   genotype:KO|cell line:AB9 GSM5393114 GSM5393114: ZEBARFISH KO AB9 Sample 20; Danio rerio; RNA Seq GSM5393114   1 RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5393114 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP324746     ZEBARFISH-KO-2_R1_001.fastq.gz ZEBARFISH-KO-2_R2_001.fastq.gz fastq fastq 9242598600.0 30808662.0 GSM5393114 r1 0:150 1:150 A:2080767915;C:2558275771;G:2525416712;T:2077571589;N:566613 150 150     2080767915 2558275771 2525416712 2077571589 566613 SRX11185276 SRS9242603 SRA1248203 GEO Max Planck Institute for heart and lung research 2 0.04236 0.04892 0.00894 0.00824 0.99811 0.99778 0.57672 0.66693 150 150 T T mates < 9% mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Germany 2021-06-20 Undetermined Undetermined Cell Line Cell Line
71391 71391 SRR21563983 SRX17566322 SRS15108370 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     10ng/mL TGFB1 treated ZMEL1 Replicate 3 GSM6579025   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing 10ng/mL TGFB1 treated ZMEL1 Replicate 3 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:TGFB1 GSM6579025 GSM6579025: 10ng/mL TGFB1 treated ZMEL1 Replicate 3; Danio rerio; RNA Seq GSM6579025 r1 GSM6579025 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN74_R1_001.fastq.gz HN74_R2_001.fastq.gz fastq fastq 10636363800.0 35454546.0 GSM6579025 r1 0:150 1:150 A:2029842779;C:3291717009;G:3355095939;T:1958873670;N:834403 150 150     2029842779 3291717009 3355095939 1958873670 834403 SRX17566322 SRS15108370     Oncology/Hematology, Boston Children's Hospital 2 0.93331 0.94647 0.18347 0.19102 0.85163 0.86429 0.71853 0.75127 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line
71392 71392 SRR21563984 SRX17566321 SRS15108369 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     10ng/mL TGFB1 treated ZMEL1 Replicate 2 GSM6579024   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing 10ng/mL TGFB1 treated ZMEL1 Replicate 2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:TGFB1 GSM6579024 GSM6579024: 10ng/mL TGFB1 treated ZMEL1 Replicate 2; Danio rerio; RNA Seq GSM6579024 r1 GSM6579024 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN73_R1_001.fastq.gz HN73_R2_001.fastq.gz fastq fastq 8998062900.0 29993543.0 GSM6579024 r1 0:150 1:150 A:1717609888;C:2782898315;G:2831578316;T:1665301010;N:675371 150 150     1717609888 2782898315 2831578316 1665301010 675371 SRX17566321 SRS15108369     Oncology/Hematology, Boston Children's Hospital 2 0.93781 0.94782 0.184 0.19138 0.8449 0.86014 0.71335 0.71676 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line
71393 71393 SRR21563985 SRX17566320 SRS15108368 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     10ng/mL TGFB1 treated ZMEL1 Replicate 1 GSM6579023   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:TGFB1|geo loc name:missing|collection date:missing 10ng/mL TGFB1 treated ZMEL1 Replicate 1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:TGFB1 GSM6579023 GSM6579023: 10ng/mL TGFB1 treated ZMEL1 Replicate 1; Danio rerio; RNA Seq GSM6579023 r1 GSM6579023 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN72_R1_001.fastq.gz HN72_R2_001.fastq.gz fastq fastq 9469796100.0 31565987.0 GSM6579023 r1 0:150 1:150 A:1779087329;C:2959081502;G:3015100670;T:1715714055;N:812544 150 150     1779087329 2959081502 3015100670 1715714055 812544 SRX17566320 SRS15108368     Oncology/Hematology, Boston Children's Hospital 2 0.93963 0.94978 0.17963 0.18558 0.84691 0.86032 0.72223 0.75653 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line
71394 71394 SRR21563986 SRX17566319 SRS15108367 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     Vehicle Control treated ZMEL1 Replicate 3 GSM6579022   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing Vehicle Control treated ZMEL1 Replicate 3 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:Vehicle GSM6579022 GSM6579022: Vehicle Control treated ZMEL1 Replicate 3; Danio rerio; RNA Seq GSM6579022 r1 GSM6579022 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN71_R1_001.fastq.gz HN71_R2_001.fastq.gz fastq fastq 7971184800.0 26570616.0 GSM6579022 r1 0:150 1:150 A:1508647225;C:2475104436;G:2532882877;T:1453950842;N:599420 150 150     1508647225 2475104436 2532882877 1453950842 599420 SRX17566319 SRS15108367     Oncology/Hematology, Boston Children's Hospital 2 0.93862 0.94897 0.18002 0.18677 0.84555 0.86198 0.7493 0.75354 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line
71395 71395 SRR21563987 SRX17566318 SRS15108366 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     Vehicle Control treated ZMEL1 Replicate 2 GSM6579021   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing Vehicle Control treated ZMEL1 Replicate 2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:Vehicle GSM6579021 GSM6579021: Vehicle Control treated ZMEL1 Replicate 2; Danio rerio; RNA Seq GSM6579021 r1 GSM6579021 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN70_R1_001.fastq.gz HN70_R2_001.fastq.gz fastq fastq 11384890800.0 37949636.0 GSM6579021 r1 0:150 1:150 A:2150820071;C:3536644295;G:3597916072;T:2098730563;N:779799 150 150     2150820071 3536644295 3597916072 2098730563 779799 SRX17566318 SRS15108366     Oncology/Hematology, Boston Children's Hospital 2 0.93899 0.94702 0.17416 0.18046 0.84147 0.85433 0.75163 0.66088 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line
71396 71396 SRR21563988 SRX17566317 SRS15108365 SRP397072 PRJNA880540 A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA seq ZMEL] GSE213328 Transcriptome Analysis Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein TIE:EGFP. EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. Single cell RNA sequencing revealed that TIE:EGFP+ melanoma cells down regulated interferon response while up regulating a novel set of chronic TGFb target genes. AP 1 factor binding is required for activation of this chronic TGFb reporter. Overexpression of the chromatin remodeler SATB2 which is associated with tumor spreading shows activation of TGFb signaling in melanoma precursor zones and early melanomas. Confocal imaging and flow cytometric analysis showed that macrophages are recruited to EGFP positive regions and preferentially phagocytose TIE:EGFP+ cells. This work identifies a TGFb induced immune response and demonstrates the need for the development of chronic TGFb biomarkers to predict patient response to TGFb inhibitors. Overall design: RNA seq +/ TGFB1 Bulk RNA seq on ZMEL1 treated with 10ng/mL TGFB1 ligand or vehicle control ZMEL1 cells were serum starved for 2 hours then treated with 10ng/mL human recombinant TGFB1 or 4mM HCl containing 1 mg/mL BSA vehicle control for an additional two hours. Experiment performed in technical triplicate. parent bioproject:PRJNA880593     Vehicle Control treated ZMEL1 Replicate 1 GSM6579020   tissue:ZMEL1 Cells|cell line:ZMEL1 Cells|treatment:Vehicle|geo loc name:missing|collection date:missing Vehicle Control treated ZMEL1 Replicate 1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to Ensembl GRCz11 whole genome using tophat 2.1 Transcript abundance were calculated with Htseq count Assembly: GRCz11 Supplementary files format and content: raw count file ZMEL1 Cells Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours. RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335. ZMEL1 were grown in filter sterilized DMEM 10% FBS 1% PenStrep 1% Glutamine at 28°C cell line:ZMEL1 Cells|treatment:Vehicle GSM6579020 GSM6579020: Vehicle Control treated ZMEL1 Replicate 1; Danio rerio; RNA Seq GSM6579020 r1 GSM6579020 1 RNA was collected from adherent cells using the Qiagen RNeasy Plus Mini Kit Qiagen #74134. One microgram of RNA was ribodepleted using NEBNext rRNA Depletion Kit NEB #E6310. Ribodepleted RNA was fragmented reverse transcribed and library prepped NEB #E7530 NEB #E7335.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP397072     HN69_R1_001.fastq.gz HN69_R2_001.fastq.gz fastq fastq 7923946200.0 26413154.0 GSM6579020 r1 0:150 1:150 A:1526034388;C:2436567275;G:2481233024;T:1479490022;N:621491 150 150     1526034388 2436567275 2481233024 1479490022 621491 SRX17566317 SRS15108365     Oncology/Hematology, Boston Children's Hospital 2 0.93823 0.94638 0.18016 0.18529 0.83481 0.84928 0.71588 0.74024 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion nebnext sc_generic bulk bulk   United States 2022-09-14 Undetermined Undetermined Cell Line Cell Line

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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");;