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 11041,ERR9995536,ERX9536682,ERS12521224,ERP138294,PRJEB53494,Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing,94bf5509-4622-4d5f-b7c5-6a14bdfac340,Other,RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome.,ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10,,dRNA seq of 4hpf Zebrafish embryos,Zebrafish dRNA 4hpf,SAMEA110422854,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110422854|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:21:01Z|INSDC last update:2022 10 10T00:21:01Z|INSDC status:public|Submitter Id:Zebrafish dRNA 4hpf|common name:zebrafish|sample name:Zebrafish dRNA 4hpf,,,,,,,,,MinION sequencing,ena EXPERIMENT TAB 27 07 2022 11:41:43:673 3,Zebrafish dRNA 4hpf,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,MinION,,ERP138294,MinION sequencing,ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|instrument model:PromethION,PDBN042841_dRNA_4hpf.tar.gz,nanopore,772304625.0,897768.0,ena RUN TAB 27 07 2022 11:41:43:690 4,0:860.25,A:224977035;C:165273397;G:156659356;T:225394837;N:0,860,,,,224977035,165273397,156659356,225394837,0,ERX9536682,ERS12521224,ERA16500713,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,3prime,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-10-10,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28539,SRR26395013,SRX22100921,SRS19166047,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,zfs:0000015 Iso seq,,strain:AB x India|age:4.7 hpf|dev stage:zfs:0000015|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 9|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: zfs:0000015,DR 009,DR 009,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,30epiboly.ccs.fq.gz,fastq,5233736965.0,1358516.0,zfs:0000015.ccs.fq.gz,0:3852.54,A:1425421240;C:1199630062;G:1191034759;T:1417650904;N:0,3852,,,,1425421240,1199630062,1191034759,1417650904,0,SRX22100921,SRS19166047,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.40862,,0.00581,,0.86123,,0.47684,,3440,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28540,SRR26395014,SRX22100920,SRS19166046,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,dome Iso seq,,strain:AB x India|age:4.3 hpf|dev stage:dome|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 8|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: dome,DR 008,DR 008,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,dome.ccs.fq.gz,fastq,6426069602.0,1667809.0,dome.ccs.fq.gz,0:3853.00,A:1735630855;C:1486999783;G:1476424228;T:1727014736;N:0,3853,,,,1735630855,1486999783,1476424228,1727014736,0,SRX22100920,SRS19166046,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.20197,,0.00145,,0.91388,,0.06247,,6938,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28541,SRR26395015,SRX22100919,SRS19166045,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,sphere Iso seq,,strain:AB x India|age:4 hpf|dev stage:sphere|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 7|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: sphere,DR 007,DR 007,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,sphere.ccs.fq.gz,fastq,7456522395.0,2030744.0,sphere.ccs.fq.gz,0:3671.82,A:2009379061;C:1725915606;G:1718055774;T:2003171954;N:0,3671,,,,2009379061,1725915606,1718055774,2003171954,0,SRX22100919,SRS19166045,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.41317,,0.00317,,0.85504,,0.46671,,5517,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28543,SRR26395017,SRX22100916,SRS19166042,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,oblong Iso seq,,strain:AB x India|age:3.7 hpf|dev stage:oblong|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 6|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: oblong,DR 006,DR 006,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,oblong.ccs.fq.gz,fastq,5138806264.0,1450821.0,oblong.ccs.fq.gz,0:3542.00,A:1387179645;C:1186984765;G:1181776562;T:1382865292;N:0,3542,,,,1387179645,1186984765,1181776562,1382865292,0,SRX22100916,SRS19166042,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.41494,,0.0019,,0.85267,,0.45513,,8789,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28551,SRR26395025,SRX22100908,SRS19166036,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep8,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 8|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate8,DR 043,DR 043,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-8_1.fq.gz C1K-8_2.fq.gz,fastq fastq,17897176360.0,63918487.0,C1K 8 1.fq.gz,0:140 1:140,A:4746019128;C:4222117801;G:4262745510;T:4666241121;N:52800,140,140,,,4746019128,4222117801,4262745510,4666241121,52800,SRX22100908,SRS19166036,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95626,0.95754,0.02383,0.02273,0.76155,0.76116,0.47882,0.47576,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28552,SRR26395026,SRX22100907,SRS19166033,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep7,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 7|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate7,DR 042,DR 042,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-7_1.fq.gz C1K-7_2.fq.gz,fastq fastq,18354684880.0,65552446.0,C1K 7 1.fq.gz,0:140 1:140,A:4895158722;C:4306679638;G:4342135666;T:4810655169;N:55685,140,140,,,4895158722,4306679638,4342135666,4810655169,55685,SRX22100907,SRS19166033,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95303,0.95677,0.02498,0.02373,0.75893,0.75866,0.47717,0.47879,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28553,SRR26395027,SRX22100906,SRS19166032,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep6,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 6|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate6,DR 041,DR 041,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-6_1.fq.gz C1K-6_2.fq.gz,fastq fastq,19129533360.0,68319762.0,C1K 6 1.fq.gz,0:140 1:140,A:5092659624;C:4497887725;G:4535246152;T:5003683373;N:56486,140,140,,,5092659624,4497887725,4535246152,5003683373,56486,SRX22100906,SRS19166032,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95423,0.95605,0.02565,0.0242,0.76086,0.76108,0.47814,0.47811,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28554,SRR26395028,SRX22100905,SRS19166031,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,high Iso seq,,strain:AB x India|age:3.3 hpf|dev stage:high|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 5|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: high,DR 005,DR 005,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,high.ccs.fq.gz,fastq,6811221417.0,1785766.0,high.ccs.fq.gz,0:3814.17,A:1820349159;C:1592171013;G:1583702800;T:1814998445;N:0,3814,,,,1820349159,1592171013,1583702800,1814998445,0,SRX22100905,SRS19166031,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.42981,,0.00073,,0.86182,,0.47846,,4404,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28555,SRR26395029,SRX22100904,SRS19166030,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep5,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 5|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate5,DR 040,DR 040,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-5_1.fq.gz C1K-5_2.fq.gz,fastq fastq,15372822080.0,54902936.0,C1K 5 1.fq.gz,0:140 1:140,A:4098626531;C:3607276129;G:3638280102;T:4028593737;N:45581,140,140,,,4098626531,3607276129,3638280102,4028593737,45581,SRX22100904,SRS19166030,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95392,0.95707,0.02512,0.02391,0.75921,0.75935,0.4795,0.47195,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28556,SRR26395030,SRX22100903,SRS19166029,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep4,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 4|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate4,DR 039,DR 039,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-4_1.fq.gz C1K-4_2.fq.gz,fastq fastq,20077595440.0,71705698.0,C1K 4 1.fq.gz,0:140 1:140,A:5379901813;C:4687577466;G:4725766166;T:5284289042;N:60953,140,140,,,5379901813,4687577466,4725766166,5284289042,60953,SRX22100903,SRS19166029,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95148,0.95674,0.02629,0.02499,0.76163,0.76155,0.48018,0.47955,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28557,SRR26395031,SRX22100902,SRS19166028,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep3,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 3|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate3,DR 038,DR 038,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-3_1.fq.gz C1K-3_2.fq.gz,fastq fastq,17934590800.0,64052110.0,C1K 3 1.fq.gz,0:140 1:140,A:4787436112;C:4203684173;G:4237881984;T:4705533453;N:55078,140,140,,,4787436112,4203684173,4237881984,4705533453,55078,SRX22100902,SRS19166028,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95381,0.95598,0.03203,0.03053,0.75586,0.75475,0.48144,0.48324,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28558,SRR26395032,SRX22100901,SRS19166027,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep2,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 2|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate2,DR 037,DR 037,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-2_2.fq.gz C1K-2_1.fq.gz,fastq fastq,19274856720.0,68838774.0,C1K 2 1.fq.gz,0:140 1:140,A:5184052449;C:4482949893;G:4518818272;T:5088977570;N:58536,140,140,,,5184052449,4482949893,4518818272,5088977570,58536,SRX22100901,SRS19166027,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.95024,0.95418,0.02706,0.02563,0.76159,0.7615,0.47685,0.47835,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28559,SRR26395033,SRX22100900,SRS19166026,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell RNA seq rep1,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:SR 1k 1|BioSampleModel:Model organism or animal,,,,,,,,,Illumina RNA seq of zebrafish: 1k cell replicate1,DR 036,DR 036,mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,HiSeq X Ten,,SRP466518,,,C1K-1_1.fq.gz C1K-1_2.fq.gz,fastq fastq,16722160840.0,59722003.0,C1K 1 1.fq.gz,0:140 1:140,A:4499833873;C:3886448032;G:3916224310;T:4419604469;N:50156,140,140,,,4499833873,3886448032,3916224310,4419604469,50156,SRX22100900,SRS19166026,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,2,0.94949,0.95361,0.02676,0.0253,0.76343,0.76313,0.48343,0.47901,140,140,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 28565,SRR26395039,SRX22100894,SRS19166020,SRP466518,PRJNA1028258,Zygotic activation of transposable elements during zebrafish early embryogenesis,PRJNA1028258,Other,Here we leverage high quality long reads plus manual annotation to establish a high resolution landscape of TE activation and transcription at the levels of locus transcript and allele over zebrafish early embryonic development. Moreover we reveal a previously unknown temporal trajectory and subcellular distribution of zygotic TE activation ZTA in zebrafish where extensive variation exists among TE families subfamilies loci transcripts and alleles with respect to evolutionary age.,,pubmed:40246845,,,1k cell Iso seq,,strain:AB x India|age:3 hpf|dev stage:1k cell|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 4|BioSampleModel:Model organism or animal,,,,,,,,,PacBio Iso seq of zebrafish: 1k cell,DR 004,DR 004,Total RNA was isolated from each developmental stages of zebrafish embryos using TRIzolTM Reagent Invitrogen. RNA purity and concentration were assessed with the NanoPhotometer spectrophotometer IMPLEN CA USA and the Qubit RNA Assay Kit in the Qubit 3.0 Fluorometer Life Technologies CA USA. The RNA integrity number RIN was determined using the RNA Nano 6000 Assay Kit and Agilent Bioanalyzer 2100 system Agilent Technologies CA USA. RNA samples with a RIN 8 were used to synthesize cDNA with SMARTerPCR cDNA Synthesis Kit Takara Bio USA Inc. Mountain View CA USA. PCR amplification was performed using a KAPA HiFi PCR Kit Kapa Biosystems Wilmington MA USA with the optimized number of cycles. Size selection of PCR products cDNA for each sample was applied using the BluePippin System: <3 kb and >3 kb. Subsequently two cDNA libraries <3 kb >3 kb were prepared using a SMRTbell Template Prep Kit 1.0 Pacific Biosciences Menlo Park CA USA and sequenced on the PacBio sequel II platform.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,PACBIO_SMRT,Sequel II,,SRP466518,,,1k.ccs.fq.gz,fastq,8036121763.0,2087907.0,1k.ccs.fq.gz,0:3848.89,A:2152838341;C:1873567602;G:1863627936;T:2146087884;N:0,3848,,,,2152838341,1873567602,1863627936,2146087884,0,SRX22100894,SRS19166020,SRA1731898,University of Michigan|Computational Medicine and Bioinformatics,University of Michigan,1,0.43117,,0.00077,,0.86352,,0.48891,,2071,,T,,long read,pacbio,pacbio_modern,full_length,poly_a,unknown,bulk,unknown,unknown,,United States,2023-10-16,Blastula,Embryo,Embryo Imprecise,All anatomical structures 29723,SRR27485668,SRX23156881,SRS20107302,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf rep4,EV06005,EV06005,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06005.R1.fastq.gz,fastq,776568876.0,10317721.0,EV06005.R1.fastq.gz,0:75.27,A:238745211;C:151859247;G:171793387;T:214113382;N:57649,75,,,,238745211,151859247,171793387,214113382,57649,SRX23156881,SRS20107302,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.87227,,0.14085,,0.81797,,0.72906,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures 29724,SRR27485669,SRX23156880,SRS20107301,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R2,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf rep4,EV06004,EV06004,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06004.R1.fastq.gz,fastq,682509965.0,9050328.0,EV06004.R1.fastq.gz,0:75.41,A:196111480;C:138950038;G:156032208;T:191368964;N:47275,75,,,,196111480,138950038,156032208,191368964,47275,SRX23156880,SRS20107301,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.91494,,0.12926,,0.80044,,0.71156,,76,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures 29728,SRR27485673,SRX23156876,SRS20107297,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf rep4,EV06012,EV06012,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06012.R1.fastq.gz,fastq,612322255.0,8128508.0,EV06012.R1.fastq.gz,0:75.33,A:190142665;C:119966127;G:131824584;T:170353082;N:35797,75,,,,190142665,119966127,131824584,170353082,35797,SRX23156876,SRS20107297,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89638,,0.12215,,0.8196,,0.79176,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures 29729,SRR27485674,SRX23156875,SRS20107296,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R3,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf rep4,EV06011,EV06011,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV06011.R1.fastq.gz,fastq,516168257.0,6849932.0,EV06011.R1.fastq.gz,0:75.35,A:157131780;C:98595108;G:111327650;T:149089977;N:23742,75,,,,157131780,98595108,111327650,149089977,23742,SRX23156875,SRS20107296,SRA1783314,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.89456,,0.0693,,0.80306,,0.73611,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-11,Blastula,Embryo,Whole Organism,All anatomical structures 29734,SRR27477294,SRX23148653,SRS20099369,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,Dome R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:5 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 5 hpf rep4,EV09005,EV09005,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09005.R1.fastq.gz,fastq,1231107704.0,16463264.0,EV09005.R1.fastq.gz,0:74.78,A:408948044;C:228823967;G:256397453;T:336404532;N:533708,74,,,,408948044,228823967,256397453,336404532,533708,SRX23148653,SRS20099369,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.84006,,0.08028,,0.80647,,0.73016,,73,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Blastula,Embryo,Whole Organism,All anatomical structures 29735,SRR27477295,SRX23148652,SRS20099365,SRP482074,PRJNA1061456,tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development,PRJNA1061456,Other,,,,,,1K cell R4,,strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:3 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of zebrafish: embryo 3 hpf rep4,EV09004,EV09004,RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP482074,,,EV09004.R1.fastq.gz,fastq,471461315.0,6271281.0,EV09004.R1.fastq.gz,0:75.18,A:148103215;C:93173628;G:103496734;T:126647635;N:40103,75,,,,148103215,93173628,103496734,126647635,40103,SRX23148652,SRS20099365,SRA1782413,Medical University of Vienna|Cell and Developmental Biology,Medical University of Vienna,1,0.87715,,0.11105,,0.80606,,0.74204,,75,,B,,usable mapping rate,illumina,nextseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,Austria,2024-01-10,Blastula,Embryo,Whole Organism,All anatomical structures 48142,SRR7749219,SRX4605277,SRS3709857,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 5 3 S4,,strain:fli1:egfp|isolate:21|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 5 3 S4,Nic MZT 2 5 3 S4,Nic MZT 2 5 3 S4,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-5-3_S4_L001_R1_001.fastq.gz,fastq,190984911.0,2538295.0,Nic MZT 2 5 3 S4 L001 R1 001.fastq.gz,0:75.24 1:0,A:52519966;C:35180627;G:44833152;T:58082446;N:368720,75,0,,,52519966,35180627,44833152,58082446,368720,SRX4605277,SRS3709857,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86935,,0.17725,,0.78815,,0.59475,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48146,SRR7749223,SRX4605273,SRS3709853,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 3 1 S2,,strain:fli1:egfp|isolate:25|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 3 1 S2,VC MZT 2 3 1 S2,VC MZT 2 3 1 S2,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-3-1_S2_L001_R1_001.fastq.gz,fastq,216452142.0,2876354.0,VC MZT 2 3 1 S2 L001 R1 001.fastq.gz,0:75.25 1:0,A:60903928;C:39226752;G:51669562;T:64341249;N:310651,75,0,,,60903928,39226752,51669562,64341249,310651,SRX4605273,SRS3709853,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86514,,0.1422,,0.78646,,0.58224,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48147,SRR7749224,SRX4605272,SRS3709852,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 3 2 S11,,strain:fli1:egfp|isolate:26|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 3 2 S11,VC MZT 2 3 2 S11,VC MZT 2 3 2 S11,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-3-2_S11_L001_R1_001.fastq.gz,fastq,207054287.0,2756810.0,VC MZT 2 3 2 S11 L001 R1 001.fastq.gz,0:75.11 1:0,A:58709487;C:38032924;G:50500441;T:59230236;N:581199,75,0,,,58709487,38032924,50500441,59230236,581199,SRX4605272,SRS3709852,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85735,,0.1637,,0.78585,,0.57361,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48148,SRR7749225,SRX4605271,SRS3709851,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 3 3 S7,,strain:fli1:egfp|isolate:27|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 3 3 S7,VC MZT 2 3 3 S7,VC MZT 2 3 3 S7,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-3-3_S7_L001_R1_001.fastq.gz,fastq,224805060.0,2985681.0,VC MZT 2 3 3 S7 L001 R1 001.fastq.gz,0:75.29 1:0,A:63036025;C:40177999;G:52296880;T:69035252;N:258904,75,0,,,63036025,40177999,52296880,69035252,258904,SRX4605271,SRS3709851,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85674,,0.14259,,0.78397,,0.56291,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48149,SRR7749226,SRX4605270,SRS3709850,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 4 1 S6,,strain:fli1:egfp|isolate:28|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 4 1 S6,VC MZT 2 4 1 S6,VC MZT 2 4 1 S6,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-4-1_S6_L001_R1_001.fastq.gz,fastq,196560073.0,2612538.0,VC MZT 2 4 1 S6 L001 R1 001.fastq.gz,0:75.24 1:0,A:55590560;C:35929491;G:46273909;T:58445414;N:320699,75,0,,,55590560,35929491,46273909,58445414,320699,SRX4605270,SRS3709850,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86257,,0.15594,,0.78494,,0.59594,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48150,SRR7749227,SRX4605269,SRS3709849,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 4 2 S4,,strain:fli1:egfp|isolate:29|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 4 2 S4,VC MZT 2 4 2 S4,VC MZT 2 4 2 S4,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-4-2_S4_L001_R1_001.fastq.gz,fastq,200868190.0,2672201.0,VC MZT 2 4 2 S4 L001 R1 001.fastq.gz,0:75.17 1:0,A:56786559;C:36707934;G:48827549;T:58051418;N:494730,75,0,,,56786559,36707934,48827549,58051418,494730,SRX4605269,SRS3709849,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86377,,0.16671,,0.7847,,0.58211,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48151,SRR7749228,SRX4605268,SRS3709848,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 4 3 S9,,strain:fli1:egfp|isolate:30|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 4 3 S9,VC MZT 2 4 3 S9,VC MZT 2 4 3 S9,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-4-3_S9_L001_R1_001.fastq.gz,fastq,237062601.0,3150637.0,VC MZT 2 4 3 S9 L001 R1 001.fastq.gz,0:75.24 1:0,A:68207913;C:41991938;G:55581570;T:70949241;N:331939,75,0,,,68207913,41991938,55581570,70949241,331939,SRX4605268,SRS3709848,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85256,,0.13608,,0.78307,,0.5771,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48162,SRR7749239,SRX4605257,SRS3709838,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 5 2 S2,,strain:fli1:egfp|isolate:20|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 5 2 S2,Nic MZT 2 5 2 S2,Nic MZT 2 5 2 S2,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-5-2_S2_L001_R1_001.fastq.gz,fastq,228343941.0,3248772.0,Nic MZT 2 5 2 S2 L001 R1 001.fastq.gz,0:70.29 1:0,A:60629793;C:39805191;G:52288409;T:61401411;N:14219137,70,0,,,60629793,39805191,52288409,61401411,14219137,SRX4605257,SRS3709838,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.84429,,0.1886,,0.79543,,0.57141,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48163,SRR7749240,SRX4605256,SRS3709836,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 5 1 S11,,strain:fli1:egfp|isolate:19|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 5 1 S11,Nic MZT 2 5 1 S11,Nic MZT 2 5 1 S11,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-5-1_S11_L001_R1_001.fastq.gz,fastq,196739500.0,2610819.0,Nic MZT 2 5 1 S11 L001 R1 001.fastq.gz,0:75.36 1:0,A:55885989;C:35230770;G:46961398;T:58619981;N:41362,75,0,,,55885989,35230770,46961398,58619981,41362,SRX4605256,SRS3709836,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85659,,0.15782,,0.7822,,0.56944,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48164,SRR7749241,SRX4605255,SRS3709837,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 4 1 S12,,strain:fli1:egfp|isolate:16|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 4 1 S12,Nic MZT 2 4 1 S12,Nic MZT 2 4 1 S12,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-4-1_S12_L001_R1_001.fastq.gz,fastq,168124767.0,2237589.0,Nic MZT 2 4 1 S12 L001 R1 001.fastq.gz,0:75.14 1:0,A:47761110;C:29995745;G:39784927;T:50158423;N:424562,75,0,,,47761110,29995745,39784927,50158423,424562,SRX4605255,SRS3709837,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85535,,0.11973,,0.78888,,0.58883,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48165,SRR7749242,SRX4605254,SRS3709835,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 3 3 S10,,strain:fli1:egfp|isolate:15|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 3 3 S10,Nic MZT 2 3 3 S10,Nic MZT 2 3 3 S10,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-3-3_S10_L001_R1_001.fastq.gz,fastq,229729299.0,3053357.0,Nic MZT 2 3 3 S10 L001 R1 001.fastq.gz,0:75.24 1:0,A:67340068;C:39924445;G:52760077;T:69473944;N:230765,75,0,,,67340068,39924445,52760077,69473944,230765,SRX4605254,SRS3709835,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.83377,,0.11349,,0.78614,,0.57112,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48166,SRR7749243,SRX4605253,SRS3709834,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 4 3 S3,,strain:fli1:egfp|isolate:18|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 4 3 S3,Nic MZT 2 4 3 S3,Nic MZT 2 4 3 S3,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-4-3_S3_L001_R1_001.fastq.gz,fastq,223794298.0,2977123.0,Nic MZT 2 4 3 S3 L001 R1 001.fastq.gz,0:75.17 1:0,A:63929699;C:41423893;G:54434009;T:63590150;N:416547,75,0,,,63929699,41423893,54434009,63590150,416547,SRX4605253,SRS3709834,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.84607,,0.17747,,0.78936,,0.58227,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48167,SRR7749244,SRX4605252,SRS3709833,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 4 2 S1,,strain:fli1:egfp|isolate:17|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 4 2 S1,Nic MZT 2 4 2 S1,Nic MZT 2 4 2 S1,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-4-2_S1_L001_R1_001.fastq.gz,fastq,210398084.0,2914697.0,Nic MZT 2 4 2 S1 L001 R1 001.fastq.gz,0:72.19 1:0,A:58211804;C:36832049;G:49094384;T:58258750;N:8001097,72,0,,,58211804,36832049,49094384,58258750,8001097,SRX4605252,SRS3709833,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85163,,0.14959,,0.78918,,0.57721,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48170,SRR7749247,SRX4605249,SRS3709830,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 3 2 S5,,strain:fli1:egfp|isolate:14|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 3 2 S5,Nic MZT 2 3 2 S5,Nic MZT 2 3 2 S5,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-3-2_S5_L001_R1_001.fastq.gz,fastq,221834813.0,2950768.0,Nic MZT 2 3 2 S5 L001 R1 001.fastq.gz,0:75.18 1:0,A:63583282;C:40135960;G:54069616;T:63589492;N:456463,75,0,,,63583282,40135960,54069616,63589492,456463,SRX4605249,SRS3709830,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85997,,0.14382,,0.78583,,0.59094,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48171,SRR7749248,SRX4605248,SRS3709829,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,Nic MZT 2 3 1 S8,,strain:fli1:egfp|isolate:13|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,Nic MZT 2 3 1 S8,Nic MZT 2 3 1 S8,Nic MZT 2 3 1 S8,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,Nic-MZT-2-3-1_S8_L001_R1_001.fastq.gz,fastq,241186165.0,3203437.0,Nic MZT 2 3 1 S8 L001 R1 001.fastq.gz,,,,,,,,,,,,SRX4605248,SRS3709829,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.83297,,0.13241,,0.781,,0.58041,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48175,SRR7749252,SRX4605244,SRS3709825,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 5 3 S3,,strain:fli1:egfp|isolate:33|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 5 3 S3,VC MZT 2 5 3 S3,VC MZT 2 5 3 S3,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-5-3_S3_L001_R1_001.fastq.gz,fastq,185035483.0,2456598.0,VC MZT 2 5 3 S3 L001 R1 001.fastq.gz,0:75.32 1:0,A:52646449;C:34075268;G:44706296;T:53569169;N:38301,75,0,,,52646449,34075268,44706296,53569169,38301,SRX4605244,SRS3709825,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.84618,,0.20107,,0.7824,,0.57961,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48176,SRR7749253,SRX4605243,SRS3709824,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 5 2 S12,,strain:fli1:egfp|isolate:32|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 5 2 S12,VC MZT 2 5 2 S12,VC MZT 2 5 2 S12,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-5-2_S12_L001_R1_001.fastq.gz,fastq,216220033.0,2872561.0,VC MZT 2 5 2 S12 L001 R1 001.fastq.gz,0:75.27 1:0,A:62300868;C:38871548;G:50500253;T:64281124;N:266240,75,0,,,62300868,38871548,50500253,64281124,266240,SRX4605243,SRS3709824,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85911,,0.16399,,0.77682,,0.60489,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48177,SRR7749254,SRX4605242,SRS3709823,SRP158697,PRJNA454154,Niclosamide Induces Epiboly Delay During Early Zebrafish Embryogenesis,PRJNA454154,Other,The objective of this project was to rely on mRNA sequencing to test the hypothesis that niclosamide interferes with pathways involved in epib progression during early zebrafish embryogenesis.,,,,,VC MZT 2 5 1 S10,,strain:fli1:egfp|isolate:31|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,VC MZT 2 5 1 S10,VC MZT 2 5 1 S10,VC MZT 2 5 1 S10,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP158697,,,VC-MZT-2-5-1_S10_L001_R1_001.fastq.gz,fastq,194194071.0,2575694.0,VC MZT 2 5 1 S10 L001 R1 001.fastq.gz,0:75.39 1:0,A:54224879;C:35623663;G:45642248;T:58656854;N:46427,75,0,,,54224879,35623663,45642248,58656854,46427,SRX4605242,SRS3709823,SRA762665,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87423,,0.18128,,0.78313,,0.60759,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-08-23,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48666,SRR7789520,SRX4644483,SRS3742550,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 5hpf 3 S8,,strain:5D|isolate:30|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 5hpf 3 S8,TDCIPP 312uM 5hpf 3 S8,TDCIPP 312uM 5hpf 3 S8,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-5hpf-3_S8_L001_R1_001.fastq.gz,fastq,301434957.0,4000726.0,TDCIPP 312uM 5hpf 3 S8 L001 R1 001.fastq.gz,0:75.35 1:0,A:90915678;C:56603137;G:73971383;T:79863909;N:80850,75,0,,,90915678,56603137,73971383,79863909,80850,SRX4644483,SRS3742550,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86911,,0.19808,,0.80868,,0.71573,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48667,SRR7789521,SRX4644482,SRS3742551,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 5hpf 2 S1,,strain:5D|isolate:29|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 5hpf 2 S1,TDCIPP 312uM 5hpf 2 S1,TDCIPP 312uM 5hpf 2 S1,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-5hpf-2_S1_L001_R1_001.fastq.gz,fastq,197729597.0,2624276.0,TDCIPP 312uM 5hpf 2 S1 L001 R1 001.fastq.gz,0:75.35 1:0,A:59990473;C:36880022;G:47774885;T:53026728;N:57489,75,0,,,59990473,36880022,47774885,53026728,57489,SRX4644482,SRS3742551,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.88116,,0.18324,,0.82353,,0.75625,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48668,SRR7789522,SRX4644481,SRS3742552,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 5hpf 2 S2,,strain:5D|isolate:26|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 5hpf 2 S2,TDCIPP 156uM 5hpf 2 S2,TDCIPP 156uM 5hpf 2 S2,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-5hpf-2_S2_L001_R1_001.fastq.gz,fastq,228760747.0,3035366.0,TDCIPP 156uM 5hpf 2 S2 L001 R1 001.fastq.gz,0:75.37 1:0,A:67940152;C:42350669;G:54760175;T:63660181;N:49570,75,0,,,67940152,42350669,54760175,63660181,49570,SRX4644481,SRS3742552,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.88323,,0.17216,,0.80975,,0.25459,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48669,SRR7789523,SRX4644480,SRS3742549,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 5hpf 1 S4,,strain:5D|isolate:25|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 5hpf 1 S4,TDCIPP 156uM 5hpf 1 S4,TDCIPP 156uM 5hpf 1 S4,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-5hpf-1_S4_L001_R1_001.fastq.gz,fastq,205893759.0,2733551.0,TDCIPP 156uM 5hpf 1 S4 L001 R1 001.fastq.gz,0:75.32 1:0,A:64189308;C:36820569;G:48195100;T:56594732;N:94050,75,0,,,64189308,36820569,48195100,56594732,94050,SRX4644480,SRS3742549,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86498,,0.16183,,0.80695,,0.72251,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48670,SRR7789524,SRX4644479,SRS3742547,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 5hpf 1 S9,,strain:5D|isolate:28|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 5hpf 1 S9,TDCIPP 312uM 5hpf 1 S9,TDCIPP 312uM 5hpf 1 S9,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-5hpf-1_S9_L001_R1_001.fastq.gz,fastq,224057988.0,2972207.0,TDCIPP 312uM 5hpf 1 S9 L001 R1 001.fastq.gz,0:75.38 1:0,A:65475098;C:41906772;G:54178001;T:62455453;N:42664,75,0,,,65475098,41906772,54178001,62455453,42664,SRX4644479,SRS3742547,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8943,,0.18439,,0.81276,,0.73409,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48671,SRR7789525,SRX4644478,SRS3742548,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 5hpf 3 S6,,strain:5D|isolate:27|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 5hpf 3 S6,TDCIPP 156uM 5hpf 3 S6,TDCIPP 156uM 5hpf 3 S6,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-5hpf-3_S6_L001_R1_001.fastq.gz,fastq,347180868.0,4609877.0,TDCIPP 156uM 5hpf 3 S6 L001 R1 001.fastq.gz,0:75.31 1:0,A:106565301;C:63385652;G:83390705;T:93736030;N:103180,75,0,,,106565301,63385652,83390705,93736030,103180,SRX4644478,SRS3742548,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.85874,,0.19122,,0.80935,,0.7272,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48672,SRR7789526,SRX4644477,SRS3742546,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 5hpf 1 S5,,strain:5D|isolate:22|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 5hpf 1 S5,DMSO 5hpf 1 S5,DMSO 5hpf 1 S5,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-5hpf-1_S5_L001_R1_001.fastq.gz,fastq,208900499.0,2771964.0,DMSO 5hpf 1 S5 L001 R1 001.fastq.gz,0:75.36 1:0,A:63534935;C:38365890;G:50190881;T:56743855;N:64938,75,0,,,63534935,38365890,50190881,56743855,64938,SRX4644477,SRS3742546,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.88006,,0.17161,,0.80771,,0.73152,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48673,SRR7789527,SRX4644476,SRS3742545,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 4hpf 3 S6,,strain:5D|isolate:21|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 4hpf 3 S6,TDCIPP 312uM 4hpf 3 S6,TDCIPP 312uM 4hpf 3 S6,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-4hpf-3_S6_L001_R1_001.fastq.gz,fastq,228701324.0,3045230.0,TDCIPP 312uM 4hpf 3 S6 L001 R1 001.fastq.gz,0:75.10 1:0,A:73866161;C:40812016;G:54842384;T:59038900;N:141863,75,0,,,73866161,40812016,54842384,59038900,141863,SRX4644476,SRS3742545,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8046,,0.15954,,0.78338,,0.65047,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48674,SRR7789528,SRX4644475,SRS3742544,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 5hpf 3 S7,,strain:5D|isolate:24|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 5hpf 3 S7,DMSO 5hpf 3 S7,DMSO 5hpf 3 S7,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-5hpf-3_S7_L001_R1_001.fastq.gz,fastq,218445719.0,2899888.0,DMSO 5hpf 3 S7 L001 R1 001.fastq.gz,0:75.33 1:0,A:64208224;C:42349017;G:55033374;T:56778155;N:76949,75,0,,,64208224,42349017,55033374,56778155,76949,SRX4644475,SRS3742544,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86641,,0.24238,,0.81379,,0.70979,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48675,SRR7789529,SRX4644474,SRS3742543,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 5hpf 2 S3,,strain:5D|isolate:23|dev stage:5 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 5hpf 2 S3,DMSO 5hpf 2 S3,DMSO 5hpf 2 S3,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-5hpf-2_S3_L001_R1_001.fastq.gz,fastq,193446245.0,2566417.0,DMSO 5hpf 2 S3 L001 R1 001.fastq.gz,0:75.38 1:0,A:56091052;C:37003463;G:48017663;T:52298069;N:35998,75,0,,,56091052,37003463,48017663,52298069,35998,SRX4644474,SRS3742543,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.88878,,0.21723,,0.81757,,0.72402,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48706,SRR7789560,SRX4644443,SRS3742513,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 3hpf 2 S3,,strain:5D|isolate:5|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 3hpf 2 S3,TDCIPP 156uM 3hpf 2 S3,TDCIPP 156uM 3hpf 2 S3,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-3hpf-2_S3_L001_R1_001.fastq.gz,fastq,231212926.0,3073504.0,TDCIPP 156uM 3hpf 2 S3 L001 R1 001.fastq.gz,0:75.23 1:0,A:70419621;C:42046395;G:54204709;T:64381669;N:160532,75,0,,,70419621,42046395,54204709,64381669,160532,SRX4644443,SRS3742513,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86625,,0.11716,,0.80371,,0.69301,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48707,SRR7789561,SRX4644442,SRS3742512,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 3hpf 3 S6,,strain:5D|isolate:6|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 3hpf 3 S6,TDCIPP 156uM 3hpf 3 S6,TDCIPP 156uM 3hpf 3 S6,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-3hpf-3_S6_L001_R1_001.fastq.gz,fastq,362932291.0,4821105.0,TDCIPP 156uM 3hpf 3 S6 L001 R1 001.fastq.gz,0:75.28 1:0,A:106222810;C:67064277;G:87594193;T:101795550;N:255461,75,0,,,106222810,67064277,87594193,101795550,255461,SRX4644442,SRS3742512,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87813,,0.13644,,0.80135,,0.66587,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48708,SRR7789562,SRX4644441,SRS3742511,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 3hpf 1 S5,,strain:5D|isolate:7|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 3hpf 1 S5,TDCIPP 312uM 3hpf 1 S5,TDCIPP 312uM 3hpf 1 S5,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-3hpf-1_S5_L001_R1_001.fastq.gz,fastq,269401256.0,3580210.0,TDCIPP 312uM 3hpf 1 S5 L001 R1 001.fastq.gz,0:75.25 1:0,A:80764488;C:48956535;G:63908853;T:75584771;N:186609,75,0,,,80764488,48956535,63908853,75584771,186609,SRX4644441,SRS3742511,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8759,,0.1086,,0.79906,,0.68477,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48709,SRR7789563,SRX4644440,SRS3742510,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 3hpf 2 S4,,strain:5D|isolate:8|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 3hpf 2 S4,TDCIPP 312uM 3hpf 2 S4,TDCIPP 312uM 3hpf 2 S4,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-3hpf-2_S4_L001_R1_001.fastq.gz,fastq,333269295.0,4433155.0,TDCIPP 312uM 3hpf 2 S4 L001 R1 001.fastq.gz,0:75.18 1:0,A:100250683;C:61646457;G:81371411;T:89669325;N:331419,75,0,,,100250683,61646457,81371411,89669325,331419,SRX4644440,SRS3742510,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86872,,0.13642,,0.80953,,0.68112,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48710,SRR7789564,SRX4644439,SRS3742509,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 3hpf 1 S9,,strain:5D|isolate:1|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 3hpf 1 S9,DMSO 3hpf 1 S9,DMSO 3hpf 1 S9,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-3hpf-1_S9_L001_R1_001.fastq.gz,fastq,345629316.0,4591488.0,DMSO 3hpf 1 S9 L001 R1 001.fastq.gz,0:75.28 1:0,A:101916167;C:63817201;G:83999559;T:95693066;N:203323,75,0,,,101916167,63817201,83999559,95693066,203323,SRX4644439,SRS3742509,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8772,,0.13606,,0.80202,,0.69007,,75,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48711,SRR7789565,SRX4644438,SRS3742507,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 3hpf 2 S7,,strain:5D|isolate:2|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 3hpf 2 S7,DMSO 3hpf 2 S7,DMSO 3hpf 2 S7,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-3hpf-2_S7_L001_R1_001.fastq.gz,fastq,234502410.0,3113290.0,DMSO 3hpf 2 S7 L001 R1 001.fastq.gz,0:75.32 1:0,A:67833938;C:42166873;G:55953453;T:68423187;N:124959,75,0,,,67833938,42166873,55953453,68423187,124959,SRX4644438,SRS3742507,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.88034,,0.14135,,0.7976,,0.66045,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48712,SRR7789566,SRX4644437,SRS3742508,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 3hpf 3 S1,,strain:5D|isolate:3|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 3hpf 3 S1,DMSO 3hpf 3 S1,DMSO 3hpf 3 S1,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-3hpf-3_S1_L001_R1_001.fastq.gz,fastq,269466625.0,3581266.0,DMSO 3hpf 3 S1 L001 R1 001.fastq.gz,0:75.24 1:0,A:80870955;C:49514830;G:65555872;T:73355131;N:169837,75,0,,,80870955,49514830,65555872,73355131,169837,SRX4644437,SRS3742508,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86206,,0.13476,,0.79803,,0.66992,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48713,SRR7789567,SRX4644436,SRS3742506,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 3hpf 1 S8,,strain:5D|isolate:4|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 3hpf 1 S8,TDCIPP 156uM 3hpf 1 S8,TDCIPP 156uM 3hpf 1 S8,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-3hpf-1_S8_L001_R1_001.fastq.gz,fastq,350344599.0,4664005.0,TDCIPP 156uM 3hpf 1 S8 L001 R1 001.fastq.gz,0:75.12 1:0,A:111607127;C:63347240;G:82500023;T:92633798;N:256411,75,0,,,111607127,63347240,82500023,92633798,256411,SRX4644436,SRS3742506,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.83041,,0.12358,,0.80551,,0.32304,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48714,SRR7789568,SRX4644435,SRS3742505,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 3hpf 3 S2,,strain:5D|isolate:9|dev stage:3 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 3hpf 3 S2,TDCIPP 312uM 3hpf 3 S2,TDCIPP 312uM 3hpf 3 S2,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-3hpf-3_S2_L001_R1_001.fastq.gz,fastq,277564815.0,3687282.0,TDCIPP 312uM 3hpf 3 S2 L001 R1 001.fastq.gz,0:75.28 1:0,A:82912366;C:50456224;G:65253764;T:78827784;N:114677,75,0,,,82912366,50456224,65253764,78827784,114677,SRX4644435,SRS3742505,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86733,,0.12257,,0.8015,,0.6662,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48715,SRR7789569,SRX4644434,SRS3742503,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 4hpf 1 S11,,strain:5D|isolate:10|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 4hpf 1 S11,DMSO 4hpf 1 S11,DMSO 4hpf 1 S11,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-4hpf-1_S11_L001_R1_001.fastq.gz,fastq,191387925.0,2539208.0,DMSO 4hpf 1 S11 L001 R1 001.fastq.gz,0:75.37 1:0,A:56221225;C:34496926;G:45630397;T:55004640;N:34737,75,0,,,56221225,34496926,45630397,55004640,34737,SRX4644434,SRS3742503,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87319,,0.14884,,0.79308,,0.69399,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48764,SRR7789618,SRX4644385,SRS3742455,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 4hpf 2 S5,,strain:5D|isolate:11|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 4hpf 2 S5,DMSO 4hpf 2 S5,DMSO 4hpf 2 S5,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-4hpf-2_S5_L001_R1_001.fastq.gz,fastq,216765839.0,2878221.0,DMSO 4hpf 2 S5 L001 R1 001.fastq.gz,0:75.31 1:0,A:66336489;C:39336393;G:50723682;T:60319136;N:50139,75,0,,,66336489,39336393,50723682,60319136,50139,SRX4644385,SRS3742455,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87082,,0.14909,,0.80016,,0.71553,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48765,SRR7789619,SRX4644384,SRS3742454,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DMSO 4hpf 3 S2,,strain:5D|isolate:12|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DMSO 4hpf 3 S2,DMSO 4hpf 3 S2,DMSO 4hpf 3 S2,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DMSO-4hpf-3_S2_L001_R1_001.fastq.gz,fastq,227754963.0,3025102.0,DMSO 4hpf 3 S2 L001 R1 001.fastq.gz,0:75.29 1:0,A:71278380;C:41288684;G:52568996;T:62535659;N:83244,75,0,,,71278380,41288684,52568996,62535659,83244,SRX4644384,SRS3742454,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8681,,0.13999,,0.80649,,0.7515,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48766,SRR7789620,SRX4644383,SRS3742453,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DorsoM 4hpf 1 S12,,strain:5D|isolate:13|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DorsoM 4hpf 1 S12,DorsoM 4hpf 1 S12,DorsoM 4hpf 1 S12,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DorsoM-4hpf-1_S12_L001_R1_001.fastq.gz,fastq,178096931.0,2363548.0,DorsoM 4hpf 1 S12 L001 R1 001.fastq.gz,0:75.35 1:0,A:52652664;C:31346970;G:42508888;T:51547187;N:41222,75,0,,,52652664,31346970,42508888,51547187,41222,SRX4644383,SRS3742453,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86668,,0.11879,,0.79204,,0.66387,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48767,SRR7789621,SRX4644382,SRS3742452,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DorsoM 4hpf 2 S7,,strain:5D|isolate:14|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DorsoM 4hpf 2 S7,DorsoM 4hpf 2 S7,DorsoM 4hpf 2 S7,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DorsoM-4hpf-2_S7_L001_R1_001.fastq.gz,fastq,163213226.0,2165635.0,DorsoM 4hpf 2 S7 L001 R1 001.fastq.gz,0:75.37 1:0,A:47915863;C:28245283;G:38380649;T:48640589;N:30842,75,0,,,47915863,28245283,38380649,48640589,30842,SRX4644382,SRS3742452,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8734,,0.1052,,0.7894,,0.66009,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48768,SRR7789622,SRX4644381,SRS3742451,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,DorsoM 4hpf 3 S1,,strain:5D|isolate:15|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DorsoM 4hpf 3 S1,DorsoM 4hpf 3 S1,DorsoM 4hpf 3 S1,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,DorsoM-4hpf-3_S1_L001_R1_001.fastq.gz,fastq,238915713.0,3170366.0,DorsoM 4hpf 3 S1 L001 R1 001.fastq.gz,0:75.36 1:0,A:69719787;C:42653236;G:56305319;T:70175619;N:61752,75,0,,,69719787,42653236,56305319,70175619,61752,SRX4644381,SRS3742451,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.86985,,0.13928,,0.79247,,0.66261,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48769,SRR7789623,SRX4644380,SRS3742450,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 4hpf 1 S9,,strain:5D|isolate:16|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 4hpf 1 S9,TDCIPP 156uM 4hpf 1 S9,TDCIPP 156uM 4hpf 1 S9,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-4hpf-1_S9_L001_R1_001.fastq.gz,fastq,205565812.0,2733033.0,TDCIPP 156uM 4hpf 1 S9 L001 R1 001.fastq.gz,0:75.22 1:0,A:64111079;C:36556135;G:48489961;T:56303912;N:104725,75,0,,,64111079,36556135,48489961,56303912,104725,SRX4644380,SRS3742450,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.84022,,0.13259,,0.80243,,0.7102,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48770,SRR7789624,SRX4644379,SRS3742449,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 4hpf 2 S4,,strain:5D|isolate:17|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 4hpf 2 S4,TDCIPP 156uM 4hpf 2 S4,TDCIPP 156uM 4hpf 2 S4,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-4hpf-2_S4_L001_R1_001.fastq.gz,fastq,143144148.0,1905396.0,TDCIPP 156uM 4hpf 2 S4 L001 R1 001.fastq.gz,0:75.13 1:0,A:47038125;C:23766078;G:33175952;T:39070353;N:93640,75,0,,,47038125,23766078,33175952,39070353,93640,SRX4644379,SRS3742449,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.81236,,0.1049,,0.80643,,0.69391,,76,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48771,SRR7789625,SRX4644378,SRS3742447,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 156uM 4hpf 3 S10,,strain:5D|isolate:18|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 156uM 4hpf 3 S10,TDCIPP 156uM 4hpf 3 S10,TDCIPP 156uM 4hpf 3 S10,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-156uM-4hpf-3_S10_L001_R1_001.fastq.gz,fastq,245717338.0,3261024.0,TDCIPP 156uM 4hpf 3 S10 L001 R1 001.fastq.gz,0:75.35 1:0,A:72279669;C:44758877;G:59271773;T:69343002;N:64017,75,0,,,72279669,44758877,59271773,69343002,64017,SRX4644378,SRS3742447,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87452,,0.15225,,0.77033,,0.67427,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48772,SRR7789626,SRX4644377,SRS3742446,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 4hpf 1 S8,,strain:5D|isolate:19|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 4hpf 1 S8,TDCIPP 312uM 4hpf 1 S8,TDCIPP 312uM 4hpf 1 S8,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-4hpf-1_S8_L001_R1_001.fastq.gz,fastq,217705695.0,2889032.0,TDCIPP 312uM 4hpf 1 S8 L001 R1 001.fastq.gz,0:75.36 1:0,A:64656510;C:40005267;G:52928505;T:60073690;N:41723,75,0,,,64656510,40005267,52928505,60073690,41723,SRX4644377,SRS3742446,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.87463,,0.16916,,0.79788,,0.70503,,73,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 48773,SRR7789627,SRX4644376,SRS3742445,SRP159670,PRJNA475635,Tris1 3 dichloro 2 propyl phosphate Exposure During Early Blastula Alters the Normal Trajectory of Zebrafish Embryogenesis,PRJNA475635,Other,The objective of this project was to rely on mRNA sequencing and amplicon sequencing to test the hypothesis that tris1 3 dichloro 2 propyl phosphate TDCIPP interferes with pathways involved in early zebrafish embryogenesis.,,,,,TDCIPP 312uM 4hpf 2 S3,,strain:5D|isolate:20|dev stage:4 hpf|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,TDCIPP 312uM 4hpf 2 S3,TDCIPP 312uM 4hpf 2 S3,TDCIPP 312uM 4hpf 2 S3,QuantSeq three prime mRNA Seq Library Prep Kit FWD,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina MiniSeq,,SRP159670,,,TDCIPP-312uM-4hpf-2_S3_L001_R1_001.fastq.gz,fastq,193829179.0,2571277.0,TDCIPP 312uM 4hpf 2 S3 L001 R1 001.fastq.gz,0:75.38 1:0,A:56878184;C:35153346;G:46042706;T:55711803;N:43140,75,0,,,56878184,35153346,46042706,55711803,43140,SRX4644376,SRS3742445,SRA767209,"University of California, Riverside|Environmental Sciences","University of California, Riverside",1,0.8801,,0.14331,,0.79584,,0.6927,,74,,B,,usable mapping rate,illumina,miseq,3prime,poly_a,lexogen,bulk,unknown,unknown,,United States,2018-09-05,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51707,SRR8791414,SRX5581197,SRS4542778,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre wide type 2,sample 6,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:Haoyu RAN|genotype:wide type|BioSampleModel:Model organism or animal,,,,,,,,,dre wide type 2,202 WT 2,202 WT 2,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,WT_3_5_9_S9_L001_R1_001.fastq.gz WT_3_5_9_S9_L001_R2_001.fastq.gz WT_3_5_9_S9_L002_R1_001.fastq.gz WT_3_5_9_S9_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3728359666.0,18551655.0,WT 3 5 9 S9 L001 R1 001.fastq.gz,0:100.50 1:100.48,A:954293388;C:880356649;G:889396693;T:997281530;N:7031406,100,100,,,954293388,880356649,889396693,997281530,7031406,SRX5581197,SRS4542778,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.9294,0.91719,0.03104,0.03129,0.75483,0.76315,0.48625,0.48351,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51708,SRR8791417,SRX5581196,SRS4542777,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre wide type 1,sample 5,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:YI CHEN|genotype:wide type|BioSampleModel:Model organism or animal,,,,,,,,,dre wide type 1,202 WT 1,202 WT 1,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,WT_3_5_8_S8_L002_R2_001.fastq.gz WT_3_5_8_S8_L001_R2_001.fastq.gz WT_3_5_8_S8_L001_R1_001.fastq.gz WT_3_5_8_S8_L002_R1_001.fastq.gz,fastq fastq fastq fastq,3541314278.0,17622215.0,WT 3 5 8 S8 L001 R1 001.fastq.gz,0:100.49 1:100.47,A:908447017;C:836934039;G:836551386;T:952578013;N:6803823,100,100,,,908447017,836934039,836551386,952578013,6803823,SRX5581196,SRS4542777,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.9438,0.93044,0.03371,0.03437,0.75288,0.76157,0.48674,0.48498,98,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51709,SRR8791415,SRX5581195,SRS4542776,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre homozygous 2,sample 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:Haoyu RAN|genotype:homozygous|BioSampleModel:Model organism or animal,,,,,,,,,dre homozygous 2,202 Ho 2,202 Ho 2,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,HOMO_3_5_2_S2_L001_R1_001.fastq.gz HOMO_3_5_2_S2_L001_R2_001.fastq.gz HOMO_3_5_2_S2_L002_R1_001.fastq.gz HOMO_3_5_2_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3565888981.0,17743517.0,HOMO 3 5 2 S2 L001 R1 001.fastq.gz,0:100.50 1:100.47,A:910268901;C:845993513;G:849351939;T:953522804;N:6751824,100,100,,,910268901,845993513,849351939,953522804,6751824,SRX5581195,SRS4542776,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.94565,0.93353,0.03202,0.03252,0.7402,0.7514,0.4884,0.48145,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51710,SRR8791416,SRX5581194,SRS4542775,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre homozygous 1,sample 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:YI CHEN|genotype:homozygous|BioSampleModel:Model organism or animal,,,,,,,,,dre homozygous 1,202 Ho 1,202 Ho 1,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,HOMO_3_5_1_S1_L001_R2_001.fastq.gz HOMO_3_5_1_S1_L002_R1_001.fastq.gz HOMO_3_5_1_S1_L002_R2_001.fastq.gz HOMO_3_5_1_S1_L001_R1_001.fastq.gz,fastq fastq fastq fastq,3477147789.0,17296169.0,HOMO 3 5 1 S1 L001 R1 001.fastq.gz,0:100.55 1:100.48,A:886198752;C:827861747;G:826981218;T:929950529;N:6155543,100,100,,,886198752,827861747,826981218,929950529,6155543,SRX5581194,SRS4542775,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.94428,0.93116,0.03377,0.03395,0.7455,0.75554,0.48586,0.47882,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51711,SRR8791418,SRX5581193,SRS4542774,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre heterozygous 2,sample 4,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:Haoyu RAN|genotype:heterozygous|BioSampleModel:Model organism or animal,,,,,,,,,dre heterozygous 2,202 He 2,202 He 2,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,HETE_3_5_6_S6_L002_R1_001.fastq.gz HETE_3_5_6_S6_L002_R2_001.fastq.gz HETE_3_5_6_S6_L001_R2_001.fastq.gz HETE_3_5_6_S6_L001_R1_001.fastq.gz,fastq fastq fastq fastq,3557055719.0,17697427.0,HETE 3 5 6 S6 L001 R1 001.fastq.gz,0:100.52 1:100.47,A:903399710;C:848399815;G:853532319;T:945118742;N:6605133,100,100,,,903399710,848399815,853532319,945118742,6605133,SRX5581193,SRS4542774,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.93462,0.92376,0.0325,0.0333,0.75213,0.7611,0.47874,0.47312,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 51712,SRR8791419,SRX5581192,SRS4542773,SRP189574,PRJNA529372,miR 202 3p is important for the early development of zebrafish embryos.,PRJNA529372,Other,The expression level of miR 202 in embryos is very low. However when knocking out miR 202 using CRISPR/Cas9 it was found that homozygous embryos died early. Further experimental research found that miR 202 3p plays a crucial role. Therefore we selected wild type heterozygous and homozygous at 3.5hpf for RNA sequencing hoping to explain the important regulation of miR 202 3p on early development of embryo.,,,,dre heterozygous 1,sample 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:3.5 hpf|sex:not applicable|tissue:embryo|collected by:YI CHEN|genotype:heterozygous|BioSampleModel:Model organism or animal,,,,,,,,,dre heterozygous 1,202 He 1,202 He 1,The first step in the workflow involves purifying the poly A containing mRNA molecules using poly T oligo attached magnetic beads. Following purification the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix SMM followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification because the polymerase used in the assay is not incorporated past this nucleotide. The addition of Actinomycin D to First Stand Synthesis Act D mix FSA prevents spurious DNA dependent synthesis while allowing RNA dependent synthesis improving strand specificity. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP189574,,,HETE_3_5_5_S5_L001_R1_001.fastq.gz HETE_3_5_5_S5_L002_R1_001.fastq.gz HETE_3_5_5_S5_L002_R2_001.fastq.gz HETE_3_5_5_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,3483801939.0,17339187.0,HETE 3 5 5 S5 L001 R1 001.fastq.gz,0:100.45 1:100.47,A:884759348;C:826704308;G:842599261;T:922711495;N:7027527,100,100,,,884759348,826704308,842599261,922711495,7027527,SRX5581192,SRS4542773,SRA866342,SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science,SHANGHAI OCEAN UNIVERSITY,2,0.94387,0.93162,0.02778,0.02889,0.75586,0.76475,0.47616,0.47765,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-04-01,Blastula,Embryo,Embryo Imprecise,All anatomical structures 61745,SRR13015603,SRX9466633,SRS7678773,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 2 4hpf.rep2,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 2 Rep2 lane2,PJ KH 012 2,PJ KH 012 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_012_S12_L002_R1_001.fastq.gz PJ_KH_012_S12_L002_R2_001.fastq.gz,fastq fastq,6248034512.0,20688856.0,PJ KH 012 S12 L002 R1 001.fastq.gz,0:151 1:151,A:1648277924;C:1474770936;G:1518949920;T:1604837292;N:1198440,151,151,,,1648277924,1474770936,1518949920,1604837292,1198440,SRX9466633,SRS7678773,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94354,0.94319,0.03242,0.03123,0.75175,0.75329,0.48435,0.48154,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61746,SRR13015604,SRX9466632,SRS7678773,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 2 4hpf.rep2,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 2 Rep2 lane1,PJ KH 012 1,PJ KH 012 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_012_S12_L001_R1_001.fastq.gz PJ_KH_012_S12_L001_R2_001.fastq.gz,fastq fastq,4720689293.0,21344802.0,PJ KH 012 S12 L001 R1 001.fastq.gz,0:151 1:151,A:1267676114;C:1099367876;G:1164875011;T:1187540955;N:1229337,151,151,,,1267676114,1099367876,1164875011,1187540955,1229337,SRX9466632,SRS7678773,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94808,0.95017,0.0318,0.03137,0.79147,0.7932,0.4792,0.47825,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61747,SRR13015605,SRX9466631,SRS7678772,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 2 4hpf.rep1,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 2 Rep1 lane2,PJ KH 011 2,PJ KH 011 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_011_S11_L002_R1_001.fastq.gz PJ_KH_011_S11_L002_R2_001.fastq.gz,fastq fastq,6431481996.0,21296298.0,PJ KH 011 S11 L002 R1 001.fastq.gz,0:151 1:151,A:1722060635;C:1495393940;G:1549727050;T:1663054022;N:1246349,151,151,,,1722060635,1495393940,1549727050,1663054022,1246349,SRX9466631,SRS7678772,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.91768,0.91808,0.03243,0.03158,0.75592,0.75783,0.48694,0.48402,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61748,SRR13015606,SRX9466630,SRS7678772,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 2 4hpf.rep1,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 2 Rep1 lane1,PJ KH 011 1,PJ KH 011 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_011_S11_L001_R1_001.fastq.gz PJ_KH_011_S11_L001_R2_001.fastq.gz,fastq fastq,6636850754.0,21976327.0,PJ KH 011 S11 L001 R1 001.fastq.gz,0:151 1:151,A:1775295087;C:1544162643;G:1601683778;T:1714026338;N:1682908,151,151,,,1775295087,1544162643,1601683778,1714026338,1682908,SRX9466630,SRS7678772,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.91734,0.91468,0.03236,0.03094,0.75597,0.7582,0.48541,0.48705,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61749,SRR13015607,SRX9466629,SRS7678771,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 1 4hpf.rep2,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 1 Rep2 lane2,PJ KH 010 2,PJ KH 010 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_010_S10_L002_R1_001.fastq.gz PJ_KH_010_S10_L002_R2_001.fastq.gz,fastq fastq,6935018978.0,22963639.0,PJ KH 010 S10 L002 R1 001.fastq.gz,0:151 1:151,A:1836339191;C:1630344337;G:1682561646;T:1784452385;N:1321419,151,151,,,1836339191,1630344337,1682561646,1784452385,1321419,SRX9466629,SRS7678771,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94856,0.94861,0.03716,0.03595,0.7502,0.75189,0.4787,0.48211,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61750,SRR13015608,SRX9466628,SRS7678771,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 1 4hpf.rep2,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 1 Rep2 lane1,PJ KH 010 1,PJ KH 010 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_010_S10_L001_R1_001.fastq.gz PJ_KH_010_S10_L001_R2_001.fastq.gz,fastq fastq,7099993726.0,23509913.0,PJ KH 010 S10 L001 R1 001.fastq.gz,0:151 1:151,A:1877827298;C:1670540865;G:1724999009;T:1824831113;N:1795441,151,151,,,1877827298,1670540865,1724999009,1824831113,1795441,SRX9466628,SRS7678771,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.94808,0.94566,0.03658,0.03564,0.74864,0.75132,0.47971,0.47662,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61751,SRR13015609,SRX9466627,SRS7678770,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 1 4hpf.rep1,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 1 Rep1 lane2,PJ KH 009 2,PJ KH 009 2,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_009_S9_L002_R1_001.fastq.gz PJ_KH_009_S9_L002_R2_001.fastq.gz,fastq fastq,6000190662.0,19868181.0,PJ KH 009 S9 L002 R1 001.fastq.gz,0:151 1:151,A:1555261055;C:1447493320;G:1497268118;T:1499028147;N:1140022,151,151,,,1555261055,1447493320,1497268118,1499028147,1140022,SRX9466627,SRS7678770,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.88464,0.88486,0.02021,0.01937,0.76033,0.76224,0.49082,0.48879,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures 61752,SRR13015610,SRX9466626,SRS7678770,SRP291905,PRJNA674002,A to I RNA editing in zebrafish during development,PRJNA674002,Other,Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.,,,,zebrafish embryos 4 hpf,single cross 1 4hpf.rep1,,strain:AB wildtype|dev stage:4 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal,,,,,,,,,mRNA seq of whole zebrafish embryos wildtype AB 4 hpf single cross 1 Rep1 lane1,PJ KH 009 1,PJ KH 009 1,stranded mRNA,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP291905,,,PJ_KH_009_S9_L001_R1_001.fastq.gz PJ_KH_009_S9_L001_R2_001.fastq.gz,fastq fastq,6314043256.0,20907428.0,PJ KH 009 S9 L001 R1 001.fastq.gz,0:151 1:151,A:1635345750;C:1523820916;G:1577386532;T:1575889430;N:1600628,151,151,,,1635345750,1523820916,1577386532,1575889430,1600628,SRX9466626,SRS7678770,SRA1153075,MDC Berlin|BIMSB,MDC Berlin,2,0.88486,0.88218,0.02054,0.0193,0.76317,0.76495,0.49004,0.48945,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Germany,2020-11-10,Blastula,Embryo,Whole Organism,All anatomical structures