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24 rows where experiment.library_layout = "SINGLE" and experiment.library_strategy = "WGS"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • WGS · 24 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • SINGLE · 24 ✖

devstage_curation_coarse 1

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
42197 42197 SRR5485641 SRX2768777 SRS2152486 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         A 3.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads A 3.0.2 A 3.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz fastq fastq 2072387100.0 20723871.0 HI.4079.001.Index 4.A R1.fastq.gz 0:100 1:0 A:539231555;C:478779687;G:466992364;T:587014266;N:369228 100 0     539231555 478779687 466992364 587014266 369228 SRX2768777 SRS2152486 SRA557480 Brandon University|Biology Brandon University 1 0.94094   0.13282   0.67566   0.46135   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42198 42198 SRR5485640 SRX2768776 SRS2152485 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         B 3.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads B 3.5.2 B 3.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz fastq fastq 2236492200.0 22364922.0 HI.4079.001.Index 5.B R1.fastq.gz 0:100 1:0 A:580646206;C:518191209;G:502712894;T:634542622;N:399269 100 0     580646206 518191209 502712894 634542622 399269 SRX2768776 SRS2152485 SRA557480 Brandon University|Biology Brandon University 1 0.94188   0.13073   0.67653   0.4635   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42199 42199 SRR5485639 SRX2768775 SRS2152484 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         C 3.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads C 3.20.2 C 3.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz fastq fastq 1979628000.0 19796280.0 HI.4079.001.Index 12.C R1.fastq.gz 0:100 1:0 A:519406228;C:453563284;G:442115002;T:564195493;N:347993 100 0     519406228 453563284 442115002 564195493 347993 SRX2768775 SRS2152484 SRA557480 Brandon University|Biology Brandon University 1 0.93946   0.14364   0.6759   0.46247   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42200 42200 SRR5485638 SRX2768774 SRS2152483 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         D 3.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads D 3.0.14 D 3.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz fastq fastq 1856095600.0 18560956.0 HI.4079.001.Index 19.D R1.fastq.gz 0:100 1:0 A:492424946;C:416504198;G:409645413;T:537196088;N:324955 100 0     492424946 416504198 409645413 537196088 324955 SRX2768774 SRS2152483 SRA557480 Brandon University|Biology Brandon University 1 0.9288   0.15497   0.69232   0.46842   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42201 42201 SRR5485637 SRX2768773 SRS2152481 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         E 3.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads E 3.5.14 E 3.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz fastq fastq 2936761500.0 29367615.0 HI.4079.001.Index 1.E R1.fastq.gz 0:100 1:0 A:762661816;C:675701333;G:661832769;T:836033713;N:531869 100 0     762661816 675701333 661832769 836033713 531869 SRX2768773 SRS2152481 SRA557480 Brandon University|Biology Brandon University 1 0.93957   0.12499   0.67714   0.4697   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42202 42202 SRR5485636 SRX2768772 SRS2152480 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         F 3.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads F 3.20.14 F 3.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz fastq fastq 2169884500.0 21698845.0 HI.4079.001.Index 3.F R1.fastq.gz 0:100 1:0 A:566808272;C:496620769;G:487930959;T:618144722;N:379778 100 0     566808272 496620769 487930959 618144722 379778 SRX2768772 SRS2152480 SRA557480 Brandon University|Biology Brandon University 1 0.93678   0.13131   0.67635   0.47972   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42203 42203 SRR5485635 SRX2768771 SRS2152482 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         G 4.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads G 4.0.2 G 4.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz fastq fastq 2008051800.0 20080518.0 HI.4079.001.Index 9.G R1.fastq.gz 0:100 1:0 A:518304309;C:466602325;G:455957803;T:566834696;N:352667 100 0     518304309 466602325 455957803 566834696 352667 SRX2768771 SRS2152482 SRA557480 Brandon University|Biology Brandon University 1 0.94445   0.12419   0.68201   0.46743   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42204 42204 SRR5485634 SRX2768770 SRS2152479 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         H 4.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads H 4.5.2 H 4.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz fastq fastq 1908097900.0 19080979.0 HI.4079.001.Index 8.H R1.fastq.gz 0:100 1:0 A:494318032;C:441931870;G:431477592;T:540030651;N:339755 100 0     494318032 441931870 431477592 540030651 339755 SRX2768770 SRS2152479 SRA557480 Brandon University|Biology Brandon University 1 0.94216   0.1306   0.68195   0.45834   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42205 42205 SRR5485633 SRX2768769 SRS2152477 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         I 4.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads I 4.20.2 I 4.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz fastq fastq 2059931100.0 20599311.0 HI.4079.001.Index 10.I R1.fastq.gz 0:100 1:0 A:536731862;C:475769707;G:462890515;T:584183211;N:355805 100 0     536731862 475769707 462890515 584183211 355805 SRX2768769 SRS2152477 SRA557480 Brandon University|Biology Brandon University 1 0.93561   0.13393   0.68225   0.46489   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42206 42206 SRR5485632 SRX2768768 SRS2152478 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         J 4.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads J 4.0.14 J 4.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz fastq fastq 2199504800.0 21995048.0 HI.4079.001.Index 11.J R1.fastq.gz 0:100 1:0 A:579625731;C:499663817;G:489173373;T:630657278;N:384601 100 0     579625731 499663817 489173373 630657278 384601 SRX2768768 SRS2152478 SRA557480 Brandon University|Biology Brandon University 1 0.93523   0.13836   0.68655   0.47839   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42207 42207 SRR5485631 SRX2768767 SRS2152475 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         K 4.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads K 4.5.14 K 4.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz fastq fastq 2154282200.0 21542822.0 HI.4079.001.Index 20.K R1.fastq.gz 0:100 1:0 A:563358732;C:494058898;G:482596638;T:613890813;N:377119 100 0     563358732 494058898 482596638 613890813 377119 SRX2768767 SRS2152475 SRA557480 Brandon University|Biology Brandon University 1 0.93863   0.12932   0.67801   0.46426   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42208 42208 SRR5485630 SRX2768766 SRS2152476 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         L 4.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads L 4.20.14 L 4.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz fastq fastq 2702515700.0 27025157.0 HI.4079.001.Index 22.L R1.fastq.gz 0:100 1:0 A:708045960;C:615042366;G:603133757;T:775807969;N:485648 100 0     708045960 615042366 603133757 775807969 485648 SRX2768766 SRS2152476 SRA557480 Brandon University|Biology Brandon University 1 0.93316   0.14421   0.68915   0.47027   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2017-05-08 Undetermined Multi-stage Trunk Surface Structure
42209 42209 SRR5485629 SRX2768765 SRS2152474 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         M 5.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads M 5.0.2 M 5.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz fastq fastq 1999183400.0 19991834.0 HI.4079.001.Index 25.M R1.fastq.gz 0:100 1:0 A:526344986;C:456726468;G:447467581;T:568292150;N:352215 100 0     526344986 456726468 447467581 568292150 352215 SRX2768765 SRS2152474 SRA557480 Brandon University|Biology Brandon University 1 0.9374   0.14185   0.67665   0.47249   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42210 42210 SRR5485628 SRX2768764 SRS2152473 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         N 5.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads N 5.5.2 N 5.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz fastq fastq 2097386100.0 20973861.0 HI.4079.001.Index 21.N R1.fastq.gz 0:100 1:0 A:551586521;C:479609380;G:467572413;T:598246436;N:371350 100 0     551586521 479609380 467572413 598246436 371350 SRX2768764 SRS2152473 SRA557480 Brandon University|Biology Brandon University 1 0.93984   0.13949   0.68219   0.46921   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42211 42211 SRR5485627 SRX2768763 SRS2152472 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         O 5.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads O 5.20.2 O 5.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz fastq fastq 2003835800.0 20038358.0 HI.4079.001.Index 23.O R1.fastq.gz 0:100 1:0 A:529075084;C:456810826;G:444441300;T:573155538;N:353052 100 0     529075084 456810826 444441300 573155538 353052 SRX2768763 SRS2152472 SRA557480 Brandon University|Biology Brandon University 1 0.93635   0.15287   0.67712   0.45807   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42212 42212 SRR5485626 SRX2768762 SRS2152471 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         P 5.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads P 5.0.14 P 5.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz fastq fastq 1799355500.0 17993555.0 HI.4079.001.Index 27.P R1.fastq.gz 0:100 1:0 A:485156399;C:399414298;G:389730888;T:524733869;N:320046 100 0     485156399 399414298 389730888 524733869 320046 SRX2768762 SRS2152471 SRA557480 Brandon University|Biology Brandon University 1 0.92813   0.15749   0.67943   0.47424   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42213 42213 SRR5485625 SRX2768761 SRS2152470 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         Q 5.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads Q 5.5.14 Q 5.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz fastq fastq 2260494100.0 22604941.0 HI.4079.001.Index 2.Q R1.fastq.gz 0:100 1:0 A:602519260;C:506296484;G:495685951;T:655587703;N:404702 100 0     602519260 506296484 495685951 655587703 404702 SRX2768761 SRS2152470 SRA557480 Brandon University|Biology Brandon University 1 0.92524   0.14979   0.6859   0.47957   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42214 42214 SRR5485624 SRX2768760 SRS2152469 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         R 5.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads R 5.20.14 R 5.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz fastq fastq 1975297900.0 19752979.0 HI.4079.001.Index 13.R R1.fastq.gz 0:100 1:0 A:527732232;C:440160233;G:430962427;T:576091914;N:351094 100 0     527732232 440160233 430962427 576091914 351094 SRX2768760 SRS2152469 SRA557480 Brandon University|Biology Brandon University 1 0.92785   0.15864   0.6814   0.47773   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42215 42215 SRR5485623 SRX2768759 SRS2152468 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         S 6.0.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads S 6.0.2 S 6.0.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz fastq fastq 2690628500.0 26906285.0 HI.4079.001.Index 6.S R1.fastq.gz 0:100 1:0 A:713021693;C:609779787;G:594591832;T:772745072;N:490116 100 0     713021693 609779787 594591832 772745072 490116 SRX2768759 SRS2152468 SRA557480 Brandon University|Biology Brandon University 1 0.93405   0.15472   0.68505   0.45796   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42216 42216 SRR5485622 SRX2768758 SRS2152466 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         T 6.5.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads T 6.5.2 T 6.5.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz fastq fastq 1949043500.0 19490435.0 HI.4079.001.Index 15.T R1.fastq.gz 0:100 1:0 A:515794596;C:441198348;G:430323928;T:561379111;N:347517 100 0     515794596 441198348 430323928 561379111 347517 SRX2768758 SRS2152466 SRA557480 Brandon University|Biology Brandon University 1 0.93579   0.16207   0.68473   0.44993   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42217 42217 SRR5485621 SRX2768757 SRS2152467 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         U 6.20.2   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads U 6.20.2 U 6.20.2 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz fastq fastq 1754851900.0 17548519.0 HI.4079.001.Index 7.U R1.fastq.gz 0:100 1:0 A:464191451;C:397313933;G:387262108;T:505777499;N:306909 100 0     464191451 397313933 387262108 505777499 306909 SRX2768757 SRS2152467 SRA557480 Brandon University|Biology Brandon University 1 0.93016   0.16163   0.68329   0.47088   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42218 42218 SRR5485620 SRX2768756 SRS2152463 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         V 6.0.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads V 6.0.14 V 6.0.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz fastq fastq 2027423200.0 20274232.0 HI.4079.001.Index 18.V R1.fastq.gz 0:100 1:0 A:542440452;C:449399743;G:440389586;T:594839784;N:353635 100 0     542440452 449399743 440389586 594839784 353635 SRX2768756 SRS2152463 SRA557480 Brandon University|Biology Brandon University 1 0.92441   0.16974   0.6842   0.48209   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42219 42219 SRR5485619 SRX2768755 SRS2152464 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         W 6.5.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads W 6.5.14 W 6.5.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz fastq fastq 2139528300.0 21395283.0 HI.4079.001.Index 14.W R1.fastq.gz 0:100 1:0 A:569259910;C:478055273;G:469309420;T:622525486;N:378211 100 0     569259910 478055273 469309420 622525486 378211 SRX2768755 SRS2152464 SRA557480 Brandon University|Biology Brandon University 1 0.92551   0.15358   0.68136   0.47093   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure
42220 42220 SRR5485618 SRX2768754 SRS2152465 SRP105410 PRJNA384462 Danio rerio Transcriptome or Gene expression PRJNA384462 Whole Genome Sequencing 5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.         X 6.20.14   ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal                 Danio rerio Raw sequence reads X 6.20.14 X 6.20.14 Illumina HiSeq read information to generate gene expression values     WGS TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2500   SRP105410     HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz fastq fastq 1768110400.0 17681104.0 HI.4079.001.Index 16.X R1.fastq.gz 0:100 1:0 A:472810124;C:392555880;G:382616900;T:519817796;N:309700 100 0     472810124 392555880 382616900 519817796 309700 SRX2768754 SRS2152465 SRA557480 Brandon University|Biology Brandon University 1 0.92486   0.16073   0.69041   0.48403   100   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Canada 2018-09-11 Undetermined Multi-stage Trunk Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;