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run_metadata

107 rows where experiment.library_layout = "PAIRED", experiment.platform = "ILLUMINA" and tissue_curation = "Cell Line"

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experiment.library_selection 4

technology 3

devstage_curation_coarse 3

devstage_curation 3

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Cell Line · 107 ✖

experiment.platform 1

  • ILLUMINA · 107 ✖

experiment.library_strategy 1

experiment.library_layout 1

  • PAIRED · 107 ✖
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
30692 30692 SRR29655998 SRX25159999 SRS21850513 SRP494129 PRJNA1085664 Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile GSE261163 Transcriptome Analysis Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.   pubmed:39584740   GC145382 HuNoV infected replicate 1 scRNAseq GSM8370069   tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing GC145382 HuNoV infected replicate 1 scRNAseq Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger Tg mpeg:mCherry   Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.   cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected GSM8370069 GSM8370069: GC145382 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq GSM8370069 r1 GSM8370069 1 Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494129     GC145382_SI-GA-B1_S1_L001_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L001_R2_001.fastq.gz fastq fastq 5781664526.0 48997157.0 GSM8370069 r1 0:28 1:90 A:1659071356;C:1268706433;G:1342749232;T:1510681009;N:456496 28 90     1659071356 1268706433 1342749232 1510681009 456496 SRX25159999 SRS21850513 SRA1913292 Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute                       T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-06-30 Larval Larval Cell Line Cell Line
30693 30693 SRR29655999 SRX25159999 SRS21850513 SRP494129 PRJNA1085664 Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile GSE261163 Transcriptome Analysis Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.   pubmed:39584740   GC145382 HuNoV infected replicate 1 scRNAseq GSM8370069   tissue:Tg mpeg:mCherry|cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing GC145382 HuNoV infected replicate 1 scRNAseq Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: hg38 Supplementary files format and content: Count Matrix Cell Ranger Tg mpeg:mCherry   Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.   cell line:Tg mpeg:mCherry|cell type:120 hpf|infection:HuNoV infected GSM8370069 GSM8370069: GC145382 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq GSM8370069 r1 GSM8370069 1 Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP494129     GC145382_SI-GA-B1_S1_L002_R1_001.fastq.gz GC145382_SI-GA-B1_S1_L002_R2_001.fastq.gz fastq fastq 6046508328.0 51241596.0 GSM8370069 r2 0:28 1:90 A:1731027394;C:1330440539;G:1408717533;T:1575870623;N:452239 28 90     1731027394 1330440539 1408717533 1575870623 452239 SRX25159999 SRS21850513 SRA1913292 Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute                       T B sc-like readlen illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-06-30 Larval Larval Cell Line Cell Line
33982 33982 SRR31022893 SRX26409990 SRS22929902 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat four:the PTA solution was exposed and cultured ttwo xxxdpf PTA PTA4   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:8|BioSampleModel:Model organism or animal                 RNA seq of zebrafish PTA4 PTA4 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     PTA4_R1.fastq.gz PTA4_R2.fastq.gz fastq fastq 8283122214.0 27427557.0 PTA4 R1.fastq.gz 0:151 1:151 A:2240001804;C:1891821306;G:1934930549;T:2215819380;N:549175 151 151     2240001804 1891821306 1934930549 2215819380 549175 SRX26409990 SRS22929902 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33983 33983 SRR31022894 SRX26409989 SRS22929901 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat three:the PTA solution was exposed and cultured ttwo xxxdpf PTA PTA3   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:7|BioSampleModel:Model organism or animal                 RNA seq of zebrafish PTA3 PTA3 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     PTA3_R1.fastq.gz PTA3_R2.fastq.gz fastq fastq 7022708604.0 23254002.0 PTA3 R1.fastq.gz 0:151 1:151 A:1891728501;C:1605352134;G:1649370849;T:1875796526;N:460594 151 151     1891728501 1605352134 1649370849 1875796526 460594 SRX26409989 SRS22929901 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33984 33984 SRR31022895 SRX26409988 SRS22929900 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat two:the PTA solution was exposed and cultured ttwo xxxdpf PTA PTA2   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:6|BioSampleModel:Model organism or animal                 RNA seq of zebrafish PTA2 PTA2 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     PTA2_R1.fastq.gz PTA2_R2.fastq.gz fastq fastq 7096338016.0 23497808.0 PTA2 R1.fastq.gz 0:151 1:151 A:1934868395;C:1599522000;G:1643956349;T:1917509746;N:481526 151 151     1934868395 1599522000 1643956349 1917509746 481526 SRX26409988 SRS22929900 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33985 33985 SRR31022896 SRX26409987 SRS22929899 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat one:the PTA solution was exposed and cultured ttwo xxxdpf PTA PTA1   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:5|BioSampleModel:Model organism or animal                 RNA seq of zebrafish PTA1 PTA1 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     PTA1_R1.fastq.gz PTA1_R2.fastq.gz fastq fastq 7610150246.0 25199173.0 PTA1 R1.fastq.gz 0:151 1:151 A:2078407024;C:1716455571;G:1761054093;T:2053740332;N:493226 151 151     2078407024 1716455571 1761054093 2053740332 493226 SRX26409987 SRS22929899 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33986 33986 SRR31022897 SRX26409986 SRS22929896 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat four:culture medium to 4dpf for sample collection Control Control4   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:4|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Control4 Control4 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     Control4_R1.fastq.gz Control4_R2.fastq.gz fastq fastq 9023764832.0 29880016.0 Control4 R1.fastq.gz 0:151 1:151 A:2384249866;C:2111349516;G:2165103194;T:2362466565;N:595691 151 151     2384249866 2111349516 2165103194 2362466565 595691 SRX26409986 SRS22929896 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33987 33987 SRR31022898 SRX26409985 SRS22929898 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat three:culture medium to 4dpf for sample collection Control Control3   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:3|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Control3 Control3 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     Control3_R1.fastq.gz Control3_R2.fastq.gz fastq fastq 8332352744.0 27590572.0 Control3 R1.fastq.gz 0:151 1:151 A:2202584495;C:1949417777;G:1998200355;T:2181578177;N:571940 151 151     2202584495 1949417777 1998200355 2181578177 571940 SRX26409985 SRS22929898 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33988 33988 SRR31022899 SRX26409984 SRS22929897 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat two:culture medium to 4dpf for sample collection Control Control2   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:2|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Control2 Control2 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     Control2_R1.fastq.gz Control2_R2.fastq.gz fastq fastq 6938613986.0 22975543.0 Control2 R1.fastq.gz 0:151 1:151 A:1833222889;C:1624373992;G:1667764740;T:1812783827;N:468538 151 151     1833222889 1624373992 1667764740 1812783827 468538 SRX26409984 SRS22929897 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
33989 33989 SRR31022900 SRX26409983 SRS22929895 SRP539058 PRJNA1173962 Study on the changes of gene transcription levels in zebrafish larvae treated to prothiobacillazole solution PRJNA1173962 Other ProthiobacillazolePTA is a kind of widely used bactericidal pesticide. Due to its high water solubility and more negative reports on aquatic organisms in recent yrs it is necessary to further study its environment.Zebrafish as an in vivo research model has its unique advantages in evaluating drug toxicity and safety as it can efficiently evaluate multiple organ toxicities at the same time. In this study the PTA exposed and Control zebrafish larvae were collected at xxxdpf for each group of 4 replicates.The sample is used for RNA seq.     Repeat one:culture medium to 4dpf for sample collection Control Control1   strain:not applicable|isolate:missing|breed:missing|cultivar:not applicable|ecotype:missing|age:4dpf stage:larval phase|collection date:2024 04|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:Fish stress response and immune response Research team|birth date:missing|birth location:missing|breeding history:missing|breeding method:missing|cell line:not applicable|cell subtype:missing|cell type:missing|collected by:ChenGuo|culture collection:missing|death date:missing|disease:missing|disease stg:missing|genotype:missing|growth protocol:missing|health state:health|isolation source:missing|lat lon:missing|phenotype:missing|sample type:missing|specimen voucher:missing|store cond:missing|stud book number:missing|treatment:missing|costumer description:1|BioSampleModel:Model organism or animal                 RNA seq of zebrafish Control1 Control1 Use the Invitrogen TRIzol kit to extract total RNA. Select total RNA with a total amount of at least 1ug and use the NEBNext Ultra II RNA Library Prep Kit for Illumina New England Biolabs Inc; Ipswich Massachusetts USA to construct sequencing libraries.     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP539058     Control1_R1.fastq.gz Control1_R2.fastq.gz fastq fastq 6383504766.0 21137433.0 Control1 R1.fastq.gz 0:151 1:151 A:1696959129;C:1488903810;G:1519707762;T:1677504326;N:429739 151 151     1696959129 1488903810 1519707762 1677504326 429739 SRX26409983 SRS22929895 SRA1992822 Nanchang University|College of Life Science Nanchang University                       B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2024-10-17 Larval Larval Cell Line Cell Line
34557 34557 SRR32105502 SRX27451095 SRS23877593 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SC2 SC2   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:10|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SC2 SC2 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301599--SC2.R1.raw.fastq.gz L1EHE2301599--SC2.R2.raw.fastq.gz fastq fastq 12846566600.0 42538300.0 L1EHE2301599 SC2.R1.raw.fastq.gz 0:151 1:151 A:3482255367;C:2921391563;G:2987736885;T:3455132712;N:50073 151 151     3482255367 2921391563 2987736885 3455132712 50073 SRX27451095 SRS23877593 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34558 34558 SRR32105503 SRX27451094 SRS23877596 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SC1 SC1   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:9|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SC1 SC1 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301598--SC1.R1.raw.fastq.gz L1EHE2301598--SC1.R2.raw.fastq.gz fastq fastq 11231331982.0 37189841.0 L1EHE2301598 SC1.R1.raw.fastq.gz 0:151 1:151 A:3065685647;C:2524957941;G:2595543794;T:3045100764;N:43836 151 151     3065685647 2524957941 2595543794 3045100764 43836 SRX27451094 SRS23877596 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34573 34573 SRR32105518 SRX27451079 SRS23877577 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SK4 SK4   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:16|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SK4 SK4 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301609--SK4.R1.raw.fastq.gz L1EHE2301609--SK4.R2.raw.fastq.gz fastq fastq 12103764380.0 40078690.0 L1EHE2301609 SK4.R1.raw.fastq.gz 0:151 1:151 A:3257453744;C:2780396394;G:2833143851;T:3232723098;N:47293 151 151     3257453744 2780396394 2833143851 3232723098 47293 SRX27451079 SRS23877577 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34574 34574 SRR32105519 SRX27451078 SRS23877576 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SK3 SK3   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:15|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SK3 SK3 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301608--SK3.R1.raw.fastq.gz L1EHE2301608--SK3.R2.raw.fastq.gz fastq fastq 13563244914.0 44911407.0 L1EHE2301608 SK3.R1.raw.fastq.gz 0:151 1:151 A:3628034105;C:3137333406;G:3198471155;T:3599351549;N:54699 151 151     3628034105 3137333406 3198471155 3599351549 54699 SRX27451078 SRS23877576 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34575 34575 SRR32105520 SRX27451077 SRS23877575 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SK2 SK2   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:14|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SK2 SK2 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301607--SK2.R1.raw.fastq.gz L1EHE2301607--SK2.R2.raw.fastq.gz fastq fastq 13308976014.0 44069457.0 L1EHE2301607 SK2.R1.raw.fastq.gz 0:151 1:151 A:3569709366;C:3066880930;G:3123966592;T:3548366304;N:52822 151 151     3569709366 3066880930 3123966592 3548366304 52822 SRX27451077 SRS23877575 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34576 34576 SRR32105521 SRX27451076 SRS23877581 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SK1 SK1   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:13|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SK1 SK1 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301606--SK1.R1.raw.fastq.gz L1EHE2301606--SK1.R2.raw.fastq.gz fastq fastq 13251027348.0 43877574.0 L1EHE2301606 SK1.R1.raw.fastq.gz 0:151 1:151 A:3562385928;C:3046618953;G:3101399402;T:3540570730;N:52335 151 151     3562385928 3046618953 3101399402 3540570730 52335 SRX27451076 SRS23877581 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34577 34577 SRR32105522 SRX27451075 SRS23877579 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SC4 SC4   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:12|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SC4 SC4 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301601--SC4.R1.raw.fastq.gz L1EHE2301601--SC4.R2.raw.fastq.gz fastq fastq 12694824888.0 42035844.0 L1EHE2301601 SC4.R1.raw.fastq.gz 0:151 1:151 A:3435956769;C:2884050436;G:2964456274;T:3410311062;N:50347 151 151     3435956769 2884050436 2964456274 3410311062 50347 SRX27451075 SRS23877579 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
34578 34578 SRR32105523 SRX27451074 SRS23877578 SRP559581 PRJNA1214993 Developmental toxicity of new psychoactive substance esketamine to zebrafish PRJNA1214993 Other New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.       SC3 SC3   breed:not applicable|age:24 hpf|collection date:2023 05 23|geo loc name:China: Guangzhou|sex:not applicable|tissue:not applicable|cell line:ZF4 cell|order:11|BioSampleModel:Model organism or animal                 Developmental toxicity of new psychoactive substance esketamine to zebrafish SC3 SC3 cell     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP559581     L1EHE2301600--SC3.R1.raw.fastq.gz L1EHE2301600--SC3.R2.raw.fastq.gz fastq fastq 12586532218.0 41677259.0 L1EHE2301600 SC3.R1.raw.fastq.gz 0:151 1:151 A:3422332578;C:2845378360;G:2913592547;T:3405179722;N:49011 151 151     3422332578 2845378360 2913592547 3405179722 49011 SRX27451074 SRS23877578 SRA2059104 South China Normal University|School of Environment South China Normal University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-01-24 Pharyngula Embryo Cell Line Cell Line
36007 36007 SRR33398626 SRX28641175 SRS24911532 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   Ca 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 21|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 212|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae Ca3 Ca3 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     Ca-3_merge.R1.fastq.gz Ca-3_merge.R2.fastq.gz fastq fastq 6737357100.0 22457857.0 Ca 3 merge.R1.fastq.gz 0:150 1:150 A:1838531075;C:1527684677;G:1561100877;T:1809740217;N:300254 150 150     1838531075 1527684677 1561100877 1809740217 300254 SRX28641175 SRS24911532 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
36008 36008 SRR33398627 SRX28641174 SRS24911531 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   Ca 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 20|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 211|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae Ca2 Ca2 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     Ca-2_merge.R1.fastq.gz Ca-2_merge.R2.fastq.gz fastq fastq 7269644400.0 24232148.0 Ca 2 merge.R1.fastq.gz 0:150 1:150 A:1977905783;C:1657807837;G:1689935893;T:1943719982;N:274905 150 150     1977905783 1657807837 1689935893 1943719982 274905 SRX28641174 SRS24911531 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
36009 36009 SRR33398628 SRX28641173 SRS24911530 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   Ca 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 19|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 210|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae Ca1 Ca1 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     Ca-1_merge.R1.fastq.gz Ca-1_merge.R2.fastq.gz fastq fastq 7116911700.0 23723039.0 Ca 1 merge.R1.fastq.gz 0:150 1:150 A:1950685415;C:1604814494;G:1640315886;T:1920831569;N:264336 150 150     1950685415 1604814494 1640315886 1920831569 264336 SRX28641173 SRS24911530 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
36010 36010 SRR33398629 SRX28641172 SRS24911529 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   WT 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 18|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 209|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae WT3 WT3 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     WT-3_merge.R1.fastq.gz WT-3_merge.R2.fastq.gz fastq fastq 6806732100.0 22689107.0 WT 3 merge.R1.fastq.gz 0:150 1:150 A:1844325028;C:1558003481;G:1585120438;T:1819030091;N:253062 150 150     1844325028 1558003481 1585120438 1819030091 253062 SRX28641172 SRS24911529 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
36011 36011 SRR33398630 SRX28641171 SRS24911528 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   WT 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 17|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 208|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae WT2 WT2 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     WT-2_merge.R1.fastq.gz WT-2_merge.R2.fastq.gz fastq fastq 9350997600.0 31169992.0 WT 2 merge.R1.fastq.gz 0:150 1:150 A:2531840914;C:2136380344;G:2177743101;T:2504682606;N:350635 150 150     2531840914 2136380344 2177743101 2504682606 350635 SRX28641171 SRS24911528 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
36012 36012 SRR33398631 SRX28641170 SRS24911527 SRP582620 PRJNA1256937 Transcriptome data of zebrafish PRJNA1256937 Other Zebrafish larvae were treated with carbimazole until 120 hpf aiming to explore the specific mechanisms by which the drug exerts toxicity on zebrafish     not collected   WT 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:120hpf|dev stage:120hpf|collection date:2024 12 16|geo loc name:China: Fujian Fuzhou|sex:not determined|tissue:Fry|biomaterial provider:Fuzhou University School of Biological Science and Engineering Institute of Life Sciences Room 207|cell line:not collected|cell type:not collected|collected by:not collected|culture collection:not collected|disease:not collected|disease stg:not collected|genotype:not collected|health state:not collected|isolation source:not collected|lat lon:not collected|phenotype:not collected|sample type:not collected|specimen voucher:not collected|store cond:not collected|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae WT1 WT1 First sample collection and processing the samples are from 5 dpf juvenile fish. Second conduct RNA extraction and quality detection. Then construct the library and perform sequencing on the machine. Finally carry out data analysis.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP582620     WT-1_merge.R1.fastq.gz WT-1_merge.R2.fastq.gz fastq fastq 8025342600.0 26751142.0 WT 1 merge.R1.fastq.gz 0:150 1:150 A:2210250425;C:1804024657;G:1840044555;T:2170729304;N:293659 150 150     2210250425 1804024657 1840044555 2170729304 293659 SRX28641170 SRS24911527 SRA2121261 Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20|Fuzhou University Fuzhou University, School of Biological Science and Engineering, Institute of Life Sciences, Room 20                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2025-05-01 Larval Larval Cell Line Cell Line
44943 44943 SRR6324387 SRX3424140 SRS2715772 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 18 30d rep3 GSM2865571   tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days ZF4 18 30d rep3 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 18 30d For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days GSM2865571 GSM2865571: ZF4 18 30d rep3; Danio rerio; RNA Seq GSM2865571   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865571 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     6_1.fq.gz 6_2.fq.gz fastq fastq 8502006300.0 28340021.0 GSM2865571 r1 0:150 1:150 A:2222321266;C:2022701531;G:2022825678;T:2234014077;N:143748 150 150     2222321266 2022701531 2022825678 2234014077 143748 SRX3424140 SRS2715772 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.92868 0.92895 0.15866 0.15599 0.74146 0.74505 0.49577 0.49894 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line
44944 44944 SRR6324386 SRX3424139 SRS2715771 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 18 30d rep2 GSM2865570   tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days ZF4 18 30d rep2 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 18 30d For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days GSM2865570 GSM2865570: ZF4 18 30d rep2; Danio rerio; RNA Seq GSM2865570   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865570 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     4_1.fq.gz 4_2.fq.gz fastq fastq 8571202200.0 28570674.0 GSM2865570 r1 0:150 1:150 A:2268978542;C:2005726985;G:2030919273;T:2265431269;N:146131 150 150     2268978542 2005726985 2030919273 2265431269 146131 SRX3424139 SRS2715771 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.92516 0.92417 0.18269 0.17989 0.73352 0.73813 0.51554 0.50598 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line
44945 44945 SRR6324385 SRX3424138 SRS2715770 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 18 30d rep1 GSM2865569   tissue:ZF4 18 30d|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days ZF4 18 30d rep1 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 18 30d For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:18°C for 30 days|sample group:cold treatment for 30 days GSM2865569 GSM2865569: ZF4 18 30d rep1; Danio rerio; RNA Seq GSM2865569   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865569 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     2_1.fq.gz 2_2.fq.gz fastq fastq 9855530100.0 32851767.0 GSM2865569 r1 0:150 1:150 A:2584345651;C:2339107553;G:2359863664;T:2572047288;N:165944 150 150     2584345651 2339107553 2359863664 2572047288 165944 SRX3424138 SRS2715770 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.92395 0.92354 0.18307 0.17869 0.73667 0.74199 0.52681 0.53689 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line
44946 44946 SRR6324384 SRX3424137 SRS2715768 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 28 rep3 GSM2865568   tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control ZF4 28 rep3 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 28 For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control GSM2865568 GSM2865568: ZF4 28 rep3; Danio rerio; RNA Seq GSM2865568   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865568 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     5_1.fq.gz 5_2.fq.gz fastq fastq 6344338200.0 21147794.0 GSM2865568 r1 0:150 1:150 A:1726699573;C:1445357744;G:1438849187;T:1733324130;N:107566 150 150     1726699573 1445357744 1438849187 1733324130 107566 SRX3424137 SRS2715768 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.9124 0.91371 0.29012 0.28803 0.73525 0.74038 0.53934 0.55133 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line
44947 44947 SRR6324383 SRX3424136 SRS2715767 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 28 rep2 GSM2865567   tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control ZF4 28 rep2 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 28 For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control GSM2865567 GSM2865567: ZF4 28 rep2; Danio rerio; RNA Seq GSM2865567   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865567 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     3_1.fq.gz 3_2.fq.gz fastq fastq 7909395600.0 26364652.0 GSM2865567 r1 0:150 1:150 A:2096969069;C:1849259032;G:1867407953;T:2095652151;N:107395 150 150     2096969069 1849259032 1867407953 2095652151 107395 SRX3424136 SRS2715767 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.90044 0.89889 0.19795 0.1953 0.73898 0.74182 0.5238 0.52236 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line
44948 44948 SRR6324382 SRX3424135 SRS2715769 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 28 rep1 GSM2865566   tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control ZF4 28 rep1 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 28 For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control GSM2865566 GSM2865566: ZF4 28 rep1; Danio rerio; RNA Seq GSM2865566   1 Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865566 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     1_2.fq.gz 1_1.fq.gz fastq fastq 9364351500.0 31214505.0 GSM2865566 r1 0:150 1:150 A:2483908747;C:2191875885;G:2204013829;T:2484392803;N:160236 150 150     2483908747 2191875885 2204013829 2484392803 160236 SRX3424135 SRS2715769 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.91474 0.91441 0.21056 0.20796 0.739 0.74477 0.52778 0.53276 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo 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
64162 64162 SRR14308451 SRX10663885 SRS8758305 SRP315996 PRJNA724011 BDE 47 zebrafish 24hpf 4dpf PRJNA724011 Other           C3   strain:AB9|age:24hpf9|dev stage:24hpf9|sex:pooled male and female|tissue:wholefish|BioSampleModel:Model organism or animal                 AB9 L9 L9 paried end seq     RNA-Seq TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA Illumina MiSeq   SRP315996     C3.raw_1.fastq.gz C3.raw_2.fastq.gz fastq fastq 6301176600.0 21003922.0 C3.raw 1.fastq.gz 0:150 1:150 A:1665737962;C:1471580978;G:1530541563;T:1633084943;N:231154 150 150     1665737962 1471580978 1530541563 1633084943 231154 SRX10663885 SRS8758305 SRA1222808 Shantou University|Medical Colleg Shantou University 2 0.93548 0.93245 0.07291 0.07262 0.76479 0.76779 0.47781 0.4799 150 150 B B biological fallback assumption illumina miseq unknown random_priming unknown bulk unknown unknown   China 2021-04-27 Pharyngula Embryo 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
74024 74024 SRR23340934 SRX19282969 SRS16684633 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       ERM H4 GSM7025527   tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing ERM H4 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:Control GSM7025527 GSM7025527: ERM H4; Danio rerio; RNA Seq GSM7025527 r1 GSM7025527 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py ERM4_1.fq.gz ERM4_2.fq.gz fastq fastq 9381788700.0 31272629.0 GSM7025527 r1 0:150 1:150 A:2457973598;C:2250509192;G:2251360794;T:2421836284;N:108832 150 150     2457973598 2250509192 2251360794 2421836284 108832 SRX19282969 SRS16684633 SRA1723725 University of Florida University of Florida 2 0.96496 0.96678 0.09461 0.09508 0.68962 0.68911 0.48319 0.48037 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74025 74025 SRR23340935 SRX19282968 SRS16684632 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       ERM H3 GSM7025526   tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing ERM H3 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:Control GSM7025526 GSM7025526: ERM H3; Danio rerio; RNA Seq GSM7025526 r1 GSM7025526 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py ERM3_1.fq.gz ERM3_2.fq.gz fastq fastq 6848962800.0 22829876.0 GSM7025526 r1 0:150 1:150 A:1832102949;C:1607836088;G:1604618541;T:1804326255;N:78967 150 150     1832102949 1607836088 1604618541 1804326255 78967 SRX19282968 SRS16684632 SRA1723725 University of Florida University of Florida 2 0.96236 0.96298 0.11466 0.11505 0.67669 0.6771 0.46065 0.47797 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74026 74026 SRR23340936 SRX19282967 SRS16684631 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       ERM H2 GSM7025525   tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing ERM H2 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:Control GSM7025525 GSM7025525: ERM H2; Danio rerio; RNA Seq GSM7025525 r1 GSM7025525 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py ERM2_1.fq.gz ERM2_2.fq.gz fastq fastq 8055333600.0 26851112.0 GSM7025525 r1 0:150 1:150 A:2174113541;C:1873627794;G:1868962308;T:2138528112;N:101845 150 150     2174113541 1873627794 1868962308 2138528112 101845 SRX19282967 SRS16684631 SRA1723725 University of Florida University of Florida 2 0.95895 0.96097 0.11791 0.11772 0.68434 0.6832 0.4604 0.46478 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74027 74027 SRR23340937 SRX19282966 SRS16684630 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       ERM H1 GSM7025524   tissue:larvae|cell line:whole larvae|treatment:Control|geo loc name:missing|collection date:missing ERM H1 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:Control GSM7025524 GSM7025524: ERM H1; Danio rerio; RNA Seq GSM7025524 r1 GSM7025524 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py ERM1_1.fq.gz ERM1_2.fq.gz fastq fastq 8012264100.0 26707547.0 GSM7025524 r1 0:150 1:150 A:2136077211;C:1883152732;G:1885576694;T:2107363535;N:93928 150 150     2136077211 1883152732 1885576694 2107363535 93928 SRX19282966 SRS16684630 SRA1723725 University of Florida University of Florida 2 0.95988 0.96103 0.12399 0.12366 0.67568 0.67639 0.47545 0.47475 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74028 74028 SRR23340938 SRX19282965 SRS16684629 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS L5 GSM7025523   tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing AVS L5 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS low dose GSM7025523 GSM7025523: AVS L5; Danio rerio; RNA Seq GSM7025523 r1 GSM7025523 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_L5_2.fq.gz AVS_L5_1.fq.gz fastq fastq 5394091800.0 17980306.0 GSM7025523 r1 0:150 1:150 A:1448537185;C:1263316442;G:1256083044;T:1426126345;N:28784 150 150     1448537185 1263316442 1256083044 1426126345 28784 SRX19282965 SRS16684629 SRA1723725 University of Florida University of Florida 2 0.95782 0.95728 0.11549 0.11583 0.67077 0.6704 0.48026 0.47831 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74029 74029 SRR23340943 SRX19282964 SRS16684628 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS L4 GSM7025522   tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing AVS L4 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS low dose GSM7025522 GSM7025522: AVS L4; Danio rerio; RNA Seq GSM7025522 r1 GSM7025522 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_L4_1.fq.gz AVS_L4_2.fq.gz fastq fastq 6218239800.0 20727466.0 GSM7025522 r1 0:150 1:150 A:1670735362;C:1455517205;G:1450471834;T:1641444300;N:71099 150 150     1670735362 1455517205 1450471834 1641444300 71099 SRX19282964 SRS16684628 SRA1723725 University of Florida University of Florida 2 0.96126 0.96248 0.13417 0.13352 0.67349 0.67367 0.47078 0.47205 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74030 74030 SRR23340939 SRX19282963 SRS16684627 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS L2 GSM7025521   tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing AVS L2 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS low dose GSM7025521 GSM7025521: AVS L2; Danio rerio; RNA Seq GSM7025521 r1 GSM7025521 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_L2_1.fq.gz AVS_L2_2.fq.gz fastq fastq 7843526400.0 26145088.0 GSM7025521 r1 0:150 1:150 A:2045499665;C:1889002910;G:1889715744;T:2019216443;N:91638 150 150     2045499665 1889002910 1889715744 2019216443 91638 SRX19282963 SRS16684627 SRA1723725 University of Florida University of Florida 2 0.96621 0.96656 0.08667 0.08617 0.68189 0.68193 0.47856 0.47892 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74031 74031 SRR23340942 SRX19282962 SRS16684626 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS L1 GSM7025520   tissue:larvae|cell line:whole larvae|treatment:AVS low dose|geo loc name:missing|collection date:missing AVS L1 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS low dose GSM7025520 GSM7025520: AVS L1; Danio rerio; RNA Seq GSM7025520 r1 GSM7025520 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_L1_1.fq.gz AVS_L1_2.fq.gz fastq fastq 8209836300.0 27366121.0 GSM7025520 r1 0:150 1:150 A:2129893804;C:1987479891;G:1991913752;T:2100452654;N:96199 150 150     2129893804 1987479891 1991913752 2100452654 96199 SRX19282962 SRS16684626 SRA1723725 University of Florida University of Florida 2 0.96585 0.96697 0.07505 0.07495 0.69992 0.7007 0.47977 0.48299 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74032 74032 SRR23340940 SRX19282961 SRS16684625 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS H4 GSM7025519   tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing AVS H4 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS high dose GSM7025519 GSM7025519: AVS H4; Danio rerio; RNA Seq GSM7025519 r1 GSM7025519 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_H4_1.fq.gz AVS_H4_2.fq.gz fastq fastq 7342444200.0 24474814.0 GSM7025519 r1 0:150 1:150 A:1937996072;C:1753867598;G:1743613654;T:1906882076;N:84800 150 150     1937996072 1753867598 1743613654 1906882076 84800 SRX19282961 SRS16684625 SRA1723725 University of Florida University of Florida 2 0.96493 0.95536 0.09819 0.097 0.69891 0.6994 0.47856 0.47909 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74033 74033 SRR23340941 SRX19282960 SRS16684624 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS H3 GSM7025518   tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing AVS H3 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS high dose GSM7025518 GSM7025518: AVS H3; Danio rerio; RNA Seq GSM7025518 r1 GSM7025518 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_H3_1.fq.gz AVS_H3_2.fq.gz fastq fastq 6872036400.0 22906788.0 GSM7025518 r1 0:150 1:150 A:1794391057;C:1653946970;G:1656595947;T:1767022732;N:79694 150 150     1794391057 1653946970 1656595947 1767022732 79694 SRX19282960 SRS16684624 SRA1723725 University of Florida University of Florida 2 0.96737 0.96839 0.086 0.0867 0.68917 0.69012 0.47371 0.4749 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74034 74034 SRR23340944 SRX19282959 SRS16684623 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS H2 GSM7025517   tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing AVS H2 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS high dose GSM7025517 GSM7025517: AVS H2; Danio rerio; RNA Seq GSM7025517 r1 GSM7025517 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_H2_1.fq.gz AVS_H2_2.fq.gz fastq fastq 4536909600.0 15123032.0 GSM7025517 r1 0:150 1:150 A:1198114288;C:1083631001;G:1079014222;T:1176097255;N:52834 150 150     1198114288 1083631001 1079014222 1176097255 52834 SRX19282959 SRS16684623 SRA1723725 University of Florida University of Florida 2 0.96395 0.96493 0.10052 0.10013 0.69832 0.69895 0.47664 0.46072 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval Cell Line Cell Line
74035 74035 SRR23340945 SRX19282958 SRS16684622 SRP420989 PRJNA931595 The effects of atorvastatin AVS and afidopyropen on developing zebrafish GSE224522 Transcriptome Analysis For RNA seq experiments 20 embryos were placed into 5 mL final volume of sterile ERM. Each treatment group were exposed within a 10 minute window. Exposure groups included ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] N=5 beakers per treatment. On 7 dpf dpf fish were transferred to a labeled and pre weighed 1.7 mL tube. The tube was then immediately flash frozen in liquid nitrogen prior to RNA seq analysis. Overall design: Exposure groups included 5 treatments: ERM [100 ng/L AVS or 1 µg/L AVS] or [100 ng/L or 1 µg/L afidopyropen] Four replicates out of the 5 were ultimately selected for RNA seq.       AVS H1 GSM7025516   tissue:larvae|cell line:whole larvae|treatment:AVS high dose|geo loc name:missing|collection date:missing AVS H1 Raw data raw reads of FASTQ format were firstly processed through fastp. In this step clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time Q20 Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website browser NCBI/UCSC/Ensembl directly. Paired end clean reads were mapped to the reference genome using HISAT2 software. Featurecounts was used to count the read numbers mapped of each gene including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. DESeq2 was used for differential expression analysis between the control and treatments. Supplementary files format and content: AVS vs ERM excel files containing read count fpkm log2 fold change p value Supplementary files format and content: Afid vs ERM excel files containing read count fpkm log2 fold change p value larvae   Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   cell line:whole larvae|treatment:AVS high dose GSM7025516 GSM7025516: AVS H1; Danio rerio; RNA Seq GSM7025516 r1 GSM7025516 1 Total RNA for each sample was isolated by using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer ThermoFisher/Invitrogen Grand Island NY and RNA quality was assessed using the Agilent 2100 Bioanalyzer Agilent Technologies Inc.. RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction. Messenger RNA was purified from total RNA using poly T oligo attached magnetic beads. post fragmentation the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis using either dUTP for directional library" Total RNA was used for mRNA isolation using the NEBNext PloyA mRNA Magnetic Isolation module New England Biolabs catalog # E7490. RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® New England Biolabs catalog #E7760 according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 Illumina Inc. CA U.S.A. Sequencing was performed by Novogene.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP420989   loader:fastq load.py AVS_H1_1.fq.gz AVS_H1_2.fq.gz fastq fastq 5335430400.0 17784768.0 GSM7025516 r1 0:150 1:150 A:1447500546;C:1236760123;G:1231786894;T:1419321777;N:61060 150 150     1447500546 1236760123 1231786894 1419321777 61060 SRX19282958 SRS16684622 SRA1723725 University of Florida University of Florida 2 0.95905 0.95961 0.13292 0.13233 0.67917 0.68069 0.48434 0.48346 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   United States 2023-02-04 Larval Larval 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");;