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,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,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,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,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,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,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,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,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,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,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,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,SRR26265244,SRX21974756,SRS19050619,SRP464312,PRJNA1022576,Danio rerio Raw sequence reads,PRJNA1022576,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis.,,,,,Control 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNAseq of zebrafish,C1,C1,normal RNA seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP464312,,,Control-1.R1.fq.gz Control-1.R2.fq.gz,fastq fastq,7005585889.0,23733330.0,Control 1.R1.fq.gz,0:147.61 1:147.57,A:1874251473;C:1620035540;G:1628125464;T:1882607735;N:565677,147,147,,,1874251473,1620035540,1628125464,1882607735,565677,SRX21974756,SRS19050619,SRA1725060,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,2,0.95539,0.95612,0.08699,0.08663,0.73777,0.73833,0.49693,0.49816,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-10-03,Undetermined,Undetermined,Cell Line,Cell Line
28470,SRR26253203,SRX21963295,SRS19039869,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 22|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND2,Small RNA IFND2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-2.deadaptor.fq.gz,fastq,278362309.0,11056139.0,IFN4 2.deadaptor.fq.gz,0:25.18,A:71944968;C:54562141;G:73333701;T:78511075;N:10424,25,,,,71944968,54562141,73333701,78511075,10424,SRX21963295,SRS19039869,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93133,,0.07401,,0.96181,,0.74558,,31,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28471,SRR26253204,SRX21963294,SRS19039868,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 21|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND1,Small RNA IFND1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-1.deadaptor.fq.gz,fastq,289362334.0,11048590.0,IFN4 1.deadaptor.fq.gz,0:26.19,A:73933649;C:59386039;G:76847534;T:79184583;N:10529,26,,,,73933649,59386039,76847534,79184583,10529,SRX21963294,SRS19039868,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91683,,0.07099,,0.96132,,0.64882,,25,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28472,SRR26253205,SRX21963293,SRS19039867,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 20|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA4,Small RNA IFNA4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-4.deadaptor.fq.gz,fastq,270529395.0,11070360.0,IFN1 4.deadaptor.fq.gz,0:24.44,A:69759888;C:54924667;G:71358091;T:74470720;N:16029,24,,,,69759888,54924667,71358091,74470720,16029,SRX21963293,SRS19039867,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.88469,,0.06696,,0.96664,,0.74853,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28473,SRR26253206,SRX21963292,SRS19039866,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 19|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA3,Small RNA IFNA3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-3.deadaptor.fq.gz,fastq,353291957.0,11740560.0,IFN1 3.deadaptor.fq.gz,0:30.09,A:89026549;C:76490337;G:94719420;T:93036955;N:18696,30,,,,89026549,76490337,94719420,93036955,18696,SRX21963292,SRS19039866,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.83151,,0.07199,,0.96471,,0.71641,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28474,SRR26253207,SRX21963291,SRS19039865,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 18|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA2,Small RNA IFNA2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-2.deadaptor.fq.gz,fastq,257949577.0,11213774.0,IFN1 2.deadaptor.fq.gz,0:23.00,A:67371681;C:51128621;G:67605590;T:71826657;N:17028,23,,,,67371681,51128621,67605590,71826657,17028,SRX21963291,SRS19039865,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91396,,0.06536,,0.97197,,0.76269,,23,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28475,SRR26253208,SRX21963290,SRS19039864,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN1 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 17|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFNA1,Small RNA IFNA1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN1-1.deadaptor.fq.gz,fastq,329358383.0,11799176.0,IFN1 1.deadaptor.fq.gz,0:27.91,A:84093681;C:68961271;G:86502739;T:89779605;N:21087,27,,,,84093681,68961271,86502739,89779605,21087,SRX21963290,SRS19039864,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.92116,,0.07483,,0.96796,,0.75179,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28476,SRR26253209,SRX21963289,SRS19039863,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 16|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C4,Small RNA C4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-4.deadaptor.fq.gz,fastq,251577736.0,10951659.0,Control 4.deadaptor.fq.gz,0:22.97,A:65382449;C:50041232;G:66038625;T:70106464;N:8966,22,,,,65382449,50041232,66038625,70106464,8966,SRX21963289,SRS19039863,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.89744,,0.06821,,0.96607,,0.63829,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28477,SRR26253210,SRX21963288,SRS19039862,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 15|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C3,Small RNA C3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-3.deadaptor.fq.gz,fastq,252164979.0,11004167.0,Control 3.deadaptor.fq.gz,0:22.92,A:65850899;C:48466665;G:66708038;T:71130786;N:8591,22,,,,65850899,48466665,66708038,71130786,8591,SRX21963288,SRS19039862,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.91567,,0.06804,,0.96278,,0.75579,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28478,SRR26253211,SRX21963287,SRS19039861,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 4,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 24|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND4,Small RNA IFND4,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-4.deadaptor.fq.gz,fastq,291708053.0,11503883.0,IFN4 4.deadaptor.fq.gz,0:25.36,A:74079231;C:61368459;G:76898572;T:79351225;N:10566,25,,,,74079231,61368459,76898572,79351225,10566,SRX21963287,SRS19039861,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.88888,,0.0633,,0.97305,,0.74862,,23,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28479,SRR26253212,SRX21963286,SRS19039860,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA IFN4 3,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 23|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA IFND3,Small RNA IFND3,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,IFN4-3.deadaptor.fq.gz,fastq,349995495.0,11885662.0,IFN4 3.deadaptor.fq.gz,0:29.45,A:87443709;C:76373108;G:92741296;T:93425866;N:11516,29,,,,87443709,76373108,92741296,93425866,11516,SRX21963286,SRS19039860,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.92619,,0.06843,,0.9709,,0.74977,,73,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28480,SRR26253213,SRX21963285,SRS19039859,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 2,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 14|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C2,Small RNA C2,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-2.deadaptor.fq.gz,fastq,254163676.0,10744164.0,Control 2.deadaptor.fq.gz,0:23.66,A:66003417;C:49309846;G:67463940;T:71377644;N:8829,23,,,,66003417,49309846,67463940,71377644,8829,SRX21963285,SRS19039859,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93068,,0.06626,,0.96441,,0.7492,,22,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
28481,SRR26253214,SRX21963284,SRS19039858,SRP464138,PRJNA1022587,Danio rerio Raw sequence reads,PRJNA1022587,Whole Genome Sequencing,In teleost  type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However  their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes   conferring cell resistance to viruses. However  the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4  ZF4 cells were stimulated with recombinant IFN1 and IFN4  and were performed transcriptome analysis of the small RNA.,,,,,Small RNA Control 1,,strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 13|BioSampleModel:Model organism or animal,,,,,,,,,Small RNAseq of zebrafish,Small RNA C1,Small RNA C1,small RNA seq of zebrafish,,,miRNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP464138,,,Control-1.deadaptor.fq.gz,fastq,267090429.0,11027241.0,Control 1.deadaptor.fq.gz,0:24.22,A:70162511;C:50705437;G:69872659;T:76339682;N:10140,24,,,,70162511,50705437,69872659,76339682,10140,SRX21963284,SRS19039858,SRA1724093,Shanghai Ocean University|College of Fisheries and Life Science,Shanghai Ocean University,1,0.93267,,0.07189,,0.96735,,0.75447,,21,,B,,usable mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-10-02,Undetermined,Undetermined,Cell Line,Cell Line
49815,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,SRR8109041,SRX4935630,SRS3979958,SRP166817,PRJNA498018,Danio rerio strain:ZFL cell line Genome sequencing,PRJNA498018,Whole Genome Sequencing,Transcriptional responses of ZFL exposed to microcystin LR,,,,sample not treated  replicate #2,ck 2,,isolate:ZFL cell line|dev stage:not applicable|sex:not applicable|tissue:cultured cell line|cell line:ZFL|cell type:epithelia|treatment:not treated  replicate #1|BioSampleModel:Model organism or animal,,,,,,,,,sample not treated  replicate #2,ck 2,ck 2,Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit Illumina according to manufacturers instructions. Three micrograms of total RNA were used as initial material for library preparation. Briefly  mRNA was purified using poly T oligo attached magnetic beads. Fragmentation of mRNA was conducted using divalent cations under elevated temperature in the Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. post adenylation of the 3 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated and the library fragments were purified using the AMPure XP system Beckman Coulter. DNA fragments with ligated adaptors on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. The products were purified AMPure XP system and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system Agilent. The sequencing libraries were then sequenced at both ends for 150 bp using a Hiseq Xten platform Illumina by Shanghai Personal Biotechnology Cp. Ltd.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP166817,,,CK-2_R2.fastq.gz CK-2_R1.fastq.gz,fastq fastq,6135368580.0,20315790.0,CK 2 R2.fastq.gz,0:151 1:151,A:1659190299;C:1402338038;G:1422425283;T:1650808795;N:606165,151,151,,,1659190299,1402338038,1422425283,1650808795,606165,SRX4935630,SRS3979958,SRA798622,Chinese Academy of Fishery Sciences|Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences,2,0.93276,0.93529,0.09768,0.1008,0.75905,0.77512,0.48616,0.50755,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,trueseq,bulk,unknown,unknown,,China,2019-01-01,Undetermined,Undetermined,Cell Line,Cell Line
64985,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,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,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,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,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,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,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,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,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,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