RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

83 rows where devstage_curation = "Blastula" and experiment.library_selection = "Oligo-dT"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.platform 3

tissue_curation 2

experiment.library_layout 2

tissue_curation_coarse 1

technology 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 83 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 83 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
11041 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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