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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
53587,SRR11886668,SRX8434202,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R3,L34024,L34024,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_GCCAAT.fastq.gz,fastq,1907555958.0,37403058.0,ws 3 1 GCCAAT.fastq.gz,0:51 1:0,A:417030128;C:470533688;G:468961155;T:550856047;N:174940,51,0,,,417030128,470533688,468961155,550856047,174940,SRX8434202,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.96213,,0.05602,,0.72967,,0.45848,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53588,SRR11886669,SRX8434201,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R2,L34023,L34023,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_ACAGTG.fastq.gz,fastq,1731933225.0,33959475.0,ws 3 1 ACAGTG.fastq.gz,0:51 1:0,A:381487795;C:424246634;G:426026749;T:500012138;N:159909,51,0,,,381487795,424246634,426026749,500012138,159909,SRX8434201,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.96269,,0.05578,,0.73261,,0.45837,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53589,SRR11886671,SRX8434200,SRS6745285,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 1dpa,,strain:AB|isolate:12|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 1dpa R1,L34022,L34022,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_TGACCA.fastq.gz,fastq,1814021907.0,35569057.0,ws 3 1 TGACCA.fastq.gz,0:51 1:0,A:404693395;C:438897306;G:444600496;T:525663505;N:167205,51,0,,,404693395,438897306,444600496,525663505,167205,SRX8434200,SRS6745285,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95686,,0.06383,,0.72677,,0.44564,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53590,SRR11886672,SRX8434199,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R3,L34021,L34021,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_TTAGGC.fastq.gz,fastq,1894657395.0,37150145.0,ws 3 1 TTAGGC.fastq.gz,0:51 1:0,A:424630121;C:461337738;G:460024108;T:548490887;N:174541,51,0,,,424630121,461337738,460024108,548490887,174541,SRX8434199,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.9524,,0.08535,,0.70999,,0.44299,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53591,SRR11886673,SRX8434198,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R2,L34020,L34020,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_CGATGT.fastq.gz,fastq,1826016036.0,35804236.0,ws 3 1 CGATGT.fastq.gz,0:51 1:0,A:408512993;C:445830968;G:443573205;T:527930321;N:168549,51,0,,,408512993,445830968,443573205,527930321,168549,SRX8434198,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95224,,0.08373,,0.70934,,0.45345,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure
53592,SRR11886674,SRX8434197,SRS6745284,SRP265421,PRJNA559885,A comparative epigenomic and single cell transcriptomic analysis of teleost regeneration,PRJNA559885,Other,The ability to regenerate body parts lost to amputation is widely but non uniformly distributed in animals. Species such as bony fishes display extensive regenerative capacities  while others such as mammals regenerate poorly. Even though regeneration has been the subject of extensive phylogenetic  developmental  cellular and molecular studies  the mechanisms underlying the broad disparity of regenerative capacities in animals remain elusive. Here we report on a comparative epigenomic and transcriptomic approach which identified an evolutionarily conserved regeneration response program in vertebrates. By defining the cis regulomes and single cell transcriptomes of early stages of regeneration in the distantly related African killifish Nothobranchius furzeri and the zebrafish Danio rerio  we uncovered species specific and evolutionarily conserved genomic responses to amputation.,,,,zebrafish fin regeneration,zebrafish fin 0dpa,,strain:AB|isolate:11|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf|dev stage:Adult|sex:not collected|tissue:caudal fin|BioSampleModel:Model organism or animal,,,,,,,,,zebrafish RNAseq 0dpa R1,L34019,L34019,Three biological replicates 6 fish per replicate were prepared for each fin regeneration time point. Ten different African killifish time points were studied including 0dpa  3hpa  6hpa  14hpa  1dpa  2dpa  3dpa  4dpa  7dpa and 18dpa. Samples from 0dpa and 1dpa were collected for zebrafish. All the freshly dissected samples used for RNA seq were quickly rinsed in cold PBS and placed in a 1.5 ml Eppendorf tube  followed by flash freezing in liquid nitrogen. Samples were then homogenized with a sterile pestle in 1 ml Trizol reagent Ambion and stored at  80 C until RNA extraction.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP265421,,,ws_3_1_ATCACG.fastq.gz,fastq,1889698206.0,37052906.0,ws 3 1 ATCACG.fastq.gz,0:51 1:0,A:425019592;C:459513661;G:459679307;T:545311781;N:173865,51,0,,,425019592,459513661,459679307,545311781,173865,SRX8434197,SRS6745284,SRA1081627,Stowers Institute for Medical Research|Sanchez lab,Stowers Institute for Medical Research,1,0.95224,,0.08995,,0.71106,,0.45283,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2020-05-31,Adult,Adult,Fin,Surface Structure