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34 rows where experiment.platform = "PACBIO_SMRT" and tissue_curation_coarse = "All anatomical structures"

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devstage_curation 8

experiment.library_strategy 2

experiment.library_selection 2

devstage_curation_coarse 2

tissue_curation_coarse 1

  • All anatomical structures · 34 ✖

tissue_curation 1

technology 1

experiment.platform 1

  • PACBIO_SMRT · 34 ✖

experiment.library_source 1

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
28538 28538 SRR26395012 SRX22100922 SRS19166048 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     50% epiboly Iso seq   strain:AB x India|age:5.3 hpf|dev stage:50% epiboly|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 10|BioSampleModel:Model organism or animal                 PacBio Iso seq of zebrafish: 50% epiboly DR 010 DR 010 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     50epiboly.ccs.fq.gz fastq 6994871304.0 1739615.0 50epiboly.ccs.fq.gz 0:4020.93 A:1886646970;C:1618863911;G:1609321304;T:1880039119;N:0 4020       1886646970 1618863911 1609321304 1880039119 0 SRX22100922 SRS19166048 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 1 0.2059   0.00164   0.92101   0.06119   3367   T   long read pacbio pacbio_modern full_length poly_a unknown bulk unknown unknown   United States 2023-10-16 Gastrula 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
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
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
28576 28576 SRR26395050 SRX22100883 SRS19166009 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     64 cell Iso seq   strain:AB x India|age:2 hpf|dev stage:64 cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 3|BioSampleModel:Model organism or animal                 PacBio Iso seq of zebrafish: 64 cell DR 003 DR 003 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   SRP466518     cell64_1.ccs.fq.gz cell64_2.ccs.fq.gz fastq fastq 2829660788.0 1238867.0 cell64 1.ccs.fq.gz 0:2284.07 A:765802910;C:646754322;G:668768985;T:748334571;N:0 2284       765802910 646754322 668768985 748334571 0 SRX22100883 SRS19166009 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 1 0.37504   0.00108   0.91149   0.48939   1913   T   long read pacbio pacbio_modern full_length poly_a unknown bulk unknown unknown   United States 2023-10-16 Cleavage Embryo Embryo Imprecise All anatomical structures
28586 28586 SRR26395062 SRX22100872 SRS19165998 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     Shield Iso seq   strain:AB x India|age:6 hpf|dev stage:shield|collection date:2021 01|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 11|BioSampleModel:Model organism or animal                 PacBio Iso seq of zebrafish: shield DR 011 DR 011 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     shield.ccs.fq.gz fastq 7256029471.0 1854553.0 shield.ccs.fq.gz 0:3912.55 A:1984833012;C:1651523494;G:1642156033;T:1977516932;N:0 3912       1984833012 1651523494 1642156033 1977516932 0 SRX22100872 SRS19165998 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 1 0.2041   0.00298   0.91837   0.08263   2962   T   long read pacbio pacbio_modern full_length poly_a unknown bulk unknown unknown   United States 2023-10-16 Gastrula Embryo Embryo Imprecise All anatomical structures
28587 28587 SRR26395063 SRX22100871 SRS19165997 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     1 cell Iso seq   strain:AB x India|age:0.5 hpf|dev stage:1cell|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 2|BioSampleModel:Model organism or animal                 PacBio Iso seq of zebrafish: 1 cell DR 002 DR 002 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   SRP466518     cell1_1.ccs.fq.gz cell1_2.ccs.fq.gz fastq fastq 2076576705.0 1053386.0 cell1 1.ccs.fq.gz 0:1971.34 A:560055059;C:479061015;G:485136981;T:552323650;N:0 1971       560055059 479061015 485136981 552323650 0 SRX22100871 SRS19165997 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 1 0.44892   0.00258   0.90114   0.50832   32   B   usable mapping rate pacbio pacbio_modern full_length poly_a unknown bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28588 28588 SRR26395064 SRX22100870 SRS19165996 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     fertilized egg Iso seq   strain:AB x India|age:0 hpf|dev stage:fertilized egg|collection date:2018 12|geo loc name:China:Beijing|sex:N/A|tissue:embryo|source material identifier:LR 1|BioSampleModel:Model organism or animal                 PacBio Iso seq of zebrafish: fertilized egg DR 001 DR 001 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   SRP466518     cell0_1.ccs.fq.gz cell0_2.ccs.fq.gz cell0_3.ccs.fq.gz fastq fastq fastq 3550605210.0 2083545.0 cell0 1.ccs.fq.gz 0:1704.12 A:990393181;C:795168216;G:861389798;T:903654015;N:0 1704       990393181 795168216 861389798 903654015 0 SRX22100870 SRS19165996 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 1 0.33296   0.00275   0.95548   0.552   1155   T   long read pacbio pacbio_modern full_length poly_a unknown bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
42960 42960 SRR5865382 SRX3033432 SRS2382228 SRP113522 PRJNA395690 High resolution annotation of Zebrafish transcriptome using long read sequencing GSE101843 Transcriptome Analysis With the emergence of zebrafish as an important model organism a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation ZGA. To date short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome the current annotation is rudimentary. By providing direct observation of full length transcripts recently refined long read sequencing platforms can dramatically improve annotation coverage and accuracy. Here we leveraged the SMRT platform to study the early ZGA stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes. Overall design: Pooled RNA of a amanitin / untreated embryos were collected and profiled with long read sequencing. Temporally corresponding pre/post ZGA pooled embryonic RNA samples were profiled with short read RNA seq. Long read raw data were assembled into transcripts using IsoSeq  PMID: 27407110 mapped to the reference GRCz10 genome using GMAP [PMID:15728110] and annotated against the reference transcriptome using Cuffcompare [PMC3334321]. Novel transcripts were compared to short read data and computationally validated in constructing a final long read augmented transcriptome.   pubmed:30061115   long reads postZGA GSM2717136   tissue:epiboly|treatment:untreated|developmental stage:6 hpf long reads postZGA Samples were run on the HiSeq2500 System and base calling and Q scoring was performed with Illumina’s Real Time Analysis RTA version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format isoforms were quantified using kallisto Genome build: GRCz10 epiboly The procedure for achieving suppression of ZGA is treatment of one to four cell embryos by injection of 0.2nmol of the RNA Polymerase inhibitor α amanitin. Pools of 15 embryos each for both untreated wild type embryos and embryos injected with 0.2nmol α amanitin to abolish zygotic transcription as described previously Zamir et al. 1997 RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina Zebrafish were maintained according to standard protocols and embryos were obtained during natural spawning of either AB TAB14 or TAB5 WT adults. The IACUC committee of the Icahn School of Medicine at Mount Sinai approved all protocols. Fertilized eggs were collected and staged based on morphological criteria to identify embryos at pre 256 cell stage and post ZGA treatment:untreated|developmental stage:6 hpf GSM2717136 GSM2717136: long reads postZGA; Danio rerio; RNA Seq GSM2717136   1 RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina GEO Accession:GSM2717136 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT PacBio RS   SRP113522   loader:fastq load.py Zebrafish_ctrl.fastq pacbio_native 84277710.0 71570.0 GSM2717136 r1   A:23712654;C:18242312;G:19552931;T:22769813;N:0         23712654 18242312 19552931 22769813 0 SRX3033432 SRS2382228 SRA591628 GEO Sealfon, Department of Neurology, Icahn School of Medicine at Mount Sinai 2 0.65823 0.65823 0.01265 0.01265 0.99904 0.99904 0.40425 0.42553 895 895 B B biological fallback assumption pacbio pacbio_early full_length rrna_depletion ribozero bulk unknown unknown   United States 2017-07-25 Gastrula Embryo Embryo Imprecise All anatomical structures
42961 42961 SRR5865381 SRX3033431 SRS2382227 SRP113522 PRJNA395690 High resolution annotation of Zebrafish transcriptome using long read sequencing GSE101843 Transcriptome Analysis With the emergence of zebrafish as an important model organism a concerted effort has been made to study its transcriptome. This effort is limited by gaps in zebrafish annotation which is especially pronounced concerning transcripts dynamically expressed during zygotic genome activation ZGA. To date short read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome the current annotation is rudimentary. By providing direct observation of full length transcripts recently refined long read sequencing platforms can dramatically improve annotation coverage and accuracy. Here we leveraged the SMRT platform to study the early ZGA stage zebrafish transcriptome. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome identifying 2748 high confidence novel transcripts that originated from previously unannotated loci and 1835 new isoforms in previously annotated genes. Overall design: Pooled RNA of a amanitin / untreated embryos were collected and profiled with long read sequencing. Temporally corresponding pre/post ZGA pooled embryonic RNA samples were profiled with short read RNA seq. Long read raw data were assembled into transcripts using IsoSeq  PMID: 27407110 mapped to the reference GRCz10 genome using GMAP [PMID:15728110] and annotated against the reference transcriptome using Cuffcompare [PMC3334321]. Novel transcripts were compared to short read data and computationally validated in constructing a final long read augmented transcriptome.   pubmed:30061115   long reads preZGA GSM2717135   tissue:256 cell|treatment:a amanitin|developmental stage:6 hpf long reads preZGA Samples were run on the HiSeq2500 System and base calling and Q scoring was performed with Illumina’s Real Time Analysis RTA version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format isoforms were quantified using kallisto Genome build: GRCz10 256 cell The procedure for achieving suppression of ZGA is treatment of one to four cell embryos by injection of 0.2nmol of the RNA Polymerase inhibitor α amanitin. Pools of 15 embryos each for both untreated wild type embryos and embryos injected with 0.2nmol α amanitin to abolish zygotic transcription as described previously Zamir et al. 1997 RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina Zebrafish were maintained according to standard protocols and embryos were obtained during natural spawning of either AB TAB14 or TAB5 WT adults. The IACUC committee of the Icahn School of Medicine at Mount Sinai approved all protocols. Fertilized eggs were collected and staged based on morphological criteria to identify embryos at pre 256 cell stage and post ZGA treatment:a amanitin|developmental stage:6 hpf GSM2717135 GSM2717135: long reads preZGA; Danio rerio; RNA Seq GSM2717135   1 RNA was isolated from zebrafish embryos via standard Trizol protocol as described Kent et al. 2016. Reverse transcription was accomplished using the Superscript III kit from Invitrogen with 2ug total RNA. RT PCR reactions were prepared with 50ng cDNA per reaction and RedTaq reverse transcriptase mix Sigma. Annealing temperature was 58° C and extension time was 3 minutes. RT qPCR reactions were prepared with 20ng cDNA per sample and set up according to the Promega GoTaq 2 Step SybrGreen™ kit using a fast 2 step protocol on the Agilent Mx3000P qPCR system and initial melting time of 3 minutes. For short read sequencing RNA was isolated from sample sets of approximately 20 embryos at 2.5 hpfand 5.25 hpf stages. RNA quality was assessed by Agilent Bioanalyzer. Samples with a RIN score of 9 or greater were used to generate cDNA libraries following treatment with the Ribo Zero rRNA removal kit Illumina GEO Accession:GSM2717135 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT PacBio RS   SRP113522   loader:fastq load.py Zebrafish_a_aman.fastq pacbio_native 90521885.0 73347.0 GSM2717135 r1   A:25481448;C:19609613;G:20975956;T:24454868;N:0         25481448 19609613 20975956 24454868 0 SRX3033431 SRS2382227 SRA591628 GEO Sealfon, Department of Neurology, Icahn School of Medicine at Mount Sinai 2 0.61069 0.61069 0.0 0.0 0.99857 0.99857 0.43661 0.43661 1668 1668 B B biological fallback assumption pacbio pacbio_early full_length rrna_depletion ribozero bulk unknown unknown   United States 2017-07-25 Gastrula Embryo Embryo Imprecise All anatomical structures
75461 75461 SRR24682216 SRX20461657 SRS17774528 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         75% epiboly   strain:AB|dev stage:75% epiboly|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 75% epiboly 75% epiboly 75% epiboly The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604104_1_r64400e_20220511_065818_2_E02.ccs.bam bam 2445533795.0 757816.0 P02TYR22604104 1 r64400e 20220511 065818 2 E02.ccs.bam 0:3227.08 A:707827290;C:530585152;G:559097725;T:648023628;N:0 3227       707827290 530585152 559097725 648023628 0 SRX20461657 SRS17774528 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.54087   0.01072   0.84772   0.44148   4236   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Gastrula Embryo Embryo Imprecise All anatomical structures
75462 75462 SRR24682217 SRX20461656 SRS17774527 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Shield   strain:AB|dev stage:Shield|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Shield Shield Shield The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604103_1_r64400e_20220511_065818_2_E02.ccs.bam bam 2465358437.0 742181.0 P02TYR22604103 1 r64400e 20220511 065818 2 E02.ccs.bam 0:3321.78 A:703901230;C:545159399;G:572405158;T:643892650;N:0 3321       703901230 545159399 572405158 643892650 0 SRX20461656 SRS17774527 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.53343   0.00627   0.84307   0.44973   3519   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Gastrula Embryo Embryo Imprecise All anatomical structures
75463 75463 SRR24682218 SRX20461655 SRS17774526 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         50% epiboly   strain:AB|dev stage:50% epiboly|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 50% epiboly 50% epiboly 50% epiboly The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604117_1_r64400e_20220511_065818_2_E02.ccs.bam bam 2347198259.0 696031.0 P02TYR22604117 1 r64400e 20220511 065818 2 E02.ccs.bam 0:3372.26 A:663704982;C:525754765;G:550887011;T:606851501;N:0 3372       663704982 525754765 550887011 606851501 0 SRX20461655 SRS17774526 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.53029   0.00409   0.84798   0.45394   3517   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Gastrula Embryo Embryo Imprecise All anatomical structures
75464 75464 SRR24682219 SRX20461654 SRS17774525 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Dome   strain:AB|dev stage:Dome|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Dome Dome Dome The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604102_1_r64400e_20220511_065818_2_E02.ccs.bam bam 3154546886.0 890787.0 P02TYR22604102 1 r64400e 20220511 065818 2 E02.ccs.bam 0:3541.30 A:897866757;C:700790757;G:734990612;T:820898760;N:0 3541       897866757 700790757 734990612 820898760 0 SRX20461654 SRS17774525 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.49522   0.00439   0.84411   0.45054   5785   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Blastula Embryo Embryo Imprecise All anatomical structures
75465 75465 SRR24682220 SRX20461653 SRS17774524 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Oblong   strain:AB|dev stage:Oblong|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Oblong Oblong Oblong The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604100_1_r64400e_20220511_065818_2_E02.ccs.bam bam 3883927264.0 1087850.0 P02TYR22604100 1 r64400e 20220511 065818 2 E02.ccs.bam 0:3570.28 A:1097185313;C:871304396;G:915871000;T:999566555;N:0 3570       1097185313 871304396 915871000 999566555 0 SRX20461653 SRS17774524 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.50563   0.00093   0.84372   0.45982   4109   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Blastula Embryo Embryo Imprecise All anatomical structures
75466 75466 SRR24682221 SRX20461652 SRS17774523 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         1k cell   strain:AB|dev stage:1k cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 1k cell 1k cell 1k cell The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604099_1_r64053_20220510_083113_3_G01.ccs.bam bam 1879917938.0 693905.0 P02TYR22604099 1 r64053 20220510 083113 3 G01.ccs.bam 0:2709.19 A:532599205;C:423737589;G:447933988;T:475647156;N:0 2709       532599205 423737589 447933988 475647156 0 SRX20461652 SRS17774523 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.60112   0.00068   0.81998   0.49181   3694   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Blastula Embryo Embryo Imprecise All anatomical structures
75467 75467 SRR24682222 SRX20461651 SRS17774522 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         128 cell   strain:AB|dev stage:128 cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 128 cell 128 cell 128 cell The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604098_1_r64053_20220510_083113_3_G01.ccs.bam bam 2358442303.0 844527.0 P02TYR22604098 1 r64053 20220510 083113 3 G01.ccs.bam 0:2792.62 A:664024741;C:534780676;G:563369243;T:596267643;N:0 2792       664024741 534780676 563369243 596267643 0 SRX20461651 SRS17774522 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.58542   0.00059   0.82688   0.49158   2312   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Blastula Embryo Embryo Imprecise All anatomical structures
75468 75468 SRR24682223 SRX20461650 SRS17774521 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Day 6   strain:AB|dev stage:Day 6|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Day 6 Day 6 Day 6 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604121_1_r64053_20220510_083113_4_H01.ccs.bam bam 3576691396.0 1042575.0 P02TYR22604121 1 r64053 20220510 083113 4 H01.ccs.bam 0:3430.63 A:1032009772;C:784907708;G:883573062;T:876200854;N:0 3430       1032009772 784907708 883573062 876200854 0 SRX20461650 SRS17774521 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.55138   0.00608   0.81343   0.43998   3611   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Larval Larval Embryo Imprecise All anatomical structures
75469 75469 SRR24682224 SRX20461649 SRS17774520 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         2 cell   strain:AB|dev stage:2 cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 2 cell 2 cell 2 cell The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604097_1_r64053_20220510_083113_3_G01.ccs.bam bam 2615775919.0 929356.0 P02TYR22604097 1 r64053 20220510 083113 3 G01.ccs.bam 0:2814.61 A:735214781;C:591950532;G:624727601;T:663883005;N:0 2814       735214781 591950532 624727601 663883005 0 SRX20461649 SRS17774520 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.58166   0.00058   0.82933   0.48648   1706   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Cleavage Embryo Embryo Imprecise All anatomical structures
75470 75470 SRR24682225 SRX20461648 SRS17774519 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Day 5   strain:AB|dev stage:Day 5|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Day 5 Day 5 Day 5 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22614797_1_r64053_20220510_083113_4_H01.ccs.bam bam 923406733.0 413841.0 P02TYR22614797 1 r64053 20220510 083113 4 H01.ccs.bam 0:2231.31 A:257122055;C:215009385;G:229534901;T:221740392;N:0 2231       257122055 215009385 229534901 221740392 0 SRX20461648 SRS17774519 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.70962   0.00154   0.83396   0.39035   1103   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Larval Larval Embryo Imprecise All anatomical structures
75471 75471 SRR24682232 SRX20461647 SRS17774518 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Day 4   strain:AB|dev stage:Day 4|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Day 4 Day 4 Day 4 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604118_1_r64053_20220510_083113_4_H01.ccs.bam bam 2334261139.0 804621.0 P02TYR22604118 1 r64053 20220510 083113 4 H01.ccs.bam 0:2901.07 A:674950884;C:505309669;G:540040111;T:613960475;N:0 2901       674950884 505309669 540040111 613960475 0 SRX20461647 SRS17774518 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.55416   0.00471   0.7876   0.47236   1761   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Larval Larval Embryo Imprecise All anatomical structures
75472 75472 SRR24682226 SRX20461646 SRS17774517 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Protruding mouth   strain:AB|dev stage:Protruding mouth|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Protruding mouth Protruding mouth Protruding mouth The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604116_1_r64053_20220510_083113_4_H01.ccs.bam bam 1077487821.0 468721.0 P02TYR22604116 1 r64053 20220510 083113 4 H01.ccs.bam 0:2298.78 A:311816839;C:236155861;G:251680246;T:277834875;N:0 2298       311816839 236155861 251680246 277834875 0 SRX20461646 SRS17774517 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.64634   0.00375   0.79699   0.49179   1337   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Larval Larval Embryo Imprecise All anatomical structures
75473 75473 SRR24682227 SRX20461645 SRS17774516 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Long pec   strain:AB|dev stage:Long pec|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Long pec Long pec Long pec The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604115_1_r64053_20220510_083113_4_H01.ccs.bam bam 1178984706.0 503711.0 P02TYR22604115 1 r64053 20220510 083113 4 H01.ccs.bam 0:2340.60 A:339563380;C:259007450;G:276316201;T:304097675;N:0 2340       339563380 259007450 276316201 304097675 0 SRX20461645 SRS17774516 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.62569   0.00525   0.80267   0.47146   1199   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Hatching Embryo Embryo Imprecise All anatomical structures
75474 75474 SRR24682228 SRX20461644 SRS17774515 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Prim 25   strain:AB|dev stage:Prim 25|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Prim 25 Prim 25 Prim 25 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604113_1_r64053_20220510_083113_4_H01.ccs.bam bam 1418704698.0 658058.0 P02TYR22604113 1 r64053 20220510 083113 4 H01.ccs.bam 0:2155.90 A:417372714;C:300192249;G:323204197;T:377935538;N:0 2155       417372714 300192249 323204197 377935538 0 SRX20461644 SRS17774515 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.62867   0.0097   0.79415   0.47483   3839   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Pharyngula Embryo Embryo Imprecise All anatomical structures
75475 75475 SRR24682229 SRX20461643 SRS17774514 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Prim 15   strain:AB|dev stage:Prim 15|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Prim 15 Prim 15 Prim 15 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604112_1_r64399e_20220512_090859_1_A02.ccs.bam bam 1383213564.0 564062.0 P02TYR22604112 1 r64399e 20220512 090859 1 A02.ccs.bam 0:2452.24 A:403982699;C:294632569;G:316412345;T:368185951;N:0 2452       403982699 294632569 316412345 368185951 0 SRX20461643 SRS17774514 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.5998   0.0069   0.79636   0.46586   2601   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Pharyngula Embryo Embryo Imprecise All anatomical structures
75476 75476 SRR24682230 SRX20461642 SRS17774513 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         Prim 5   strain:AB|dev stage:Prim 5|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: Prim 5 Prim 5 Prim 5 The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604110_1_r64399e_20220512_090859_1_A02.ccs.bam bam 1245119132.0 541632.0 P02TYR22604110 1 r64399e 20220512 090859 1 A02.ccs.bam 0:2298.83 A:367833391;C:262003404;G:283350026;T:331932311;N:0 2298       367833391 262003404 283350026 331932311 0 SRX20461642 SRS17774513 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.62578   0.00824   0.79669   0.47095   636   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Pharyngula Embryo Embryo Imprecise All anatomical structures
75477 75477 SRR24682231 SRX20461641 SRS17774512 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         20 25 Somites   strain:AB|dev stage:20 25 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 20 25 Somites 20 25 Somites 20 25 Somites The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604108_1_r64399e_20220512_090859_1_A02.ccs.bam bam 2078794793.0 725960.0 P02TYR22604108 1 r64399e 20220512 090859 1 A02.ccs.bam 0:2863.51 A:605292389;C:441948349;G:472618370;T:558935685;N:0 2863       605292389 441948349 472618370 558935685 0 SRX20461641 SRS17774512 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.55105   0.00964   0.80831   0.45443   1451   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Segmentation Embryo Embryo Imprecise All anatomical structures
75478 75478 SRR24682233 SRX20461640 SRS17774511 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         14 19 Somites   strain:AB|dev stage:14 19 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 14 19 Somites 14 19 Somites 14 19 Somites The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604106_1_r64399e_20220512_090859_1_A02.ccs.bam bam 2511998751.0 864091.0 P02TYR22604106 1 r64399e 20220512 090859 1 A02.ccs.bam 0:2907.10 A:730743897;C:535154858;G:572074928;T:674025068;N:0 2907       730743897 535154858 572074928 674025068 0 SRX20461640 SRS17774511 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.54959   0.01154   0.816   0.44689   2262   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Segmentation Embryo Embryo Imprecise All anatomical structures
75479 75479 SRR24682234 SRX20461639 SRS17774510 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         1 4 Somites   strain:AB|dev stage:1 4 Somites|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 1 4 Somites 1 4 Somites 1 4 Somites The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604105_1_r64399e_20220512_090859_1_A02.ccs.bam bam 2199775856.0 820475.0 P02TYR22604105 1 r64399e 20220512 090859 1 A02.ccs.bam 0:2681.10 A:637639661;C:475508465;G:505308978;T:581318752;N:0 2681       637639661 475508465 505308978 581318752 0 SRX20461639 SRS17774510 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.60261   0.00759   0.83583   0.49086   1389   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Segmentation Embryo Embryo Imprecise All anatomical structures
75480 75480 SRR24682235 SRX20461638 SRS17774509 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         1 cell   strain:AB|dev stage:1cell|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: 1 cell 1 cell 1 cell The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22604096_1_r64053_20220510_083113_3_G01.ccs.bam bam 2275468478.0 775186.0 P02TYR22604096 1 r64053 20220510 083113 3 G01.ccs.bam 0:2935.38 A:638155276;C:516035520;G:543447739;T:577829943;N:0 2935       638155276 516035520 543447739 577829943 0 SRX20461638 SRS17774509 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.56682   0.00066   0.82994   0.48167   1465   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Zygote Embryo Embryo Imprecise All anatomical structures
75481 75481 SRR24682236 SRX20461637 SRS17774508 SRP438861 PRJNA973729 Danio rerio strain:AB Raw sequence reads PRJNA973729 Other Full length transcriptome at 21 developmental stages during embryonic development of Zebrafish.         unfertilized   strain:AB|dev stage:unfertilized|sex:not determined|tissue:embryo|BioSampleModel:Model organism or animal                 full length transcriptome of Danio rerio: unfertilized unfertilized unfertilized The RNA of each sample was reversely transcribed into cDNA using a SMARTer PCR cDNA Synthesis Kit. Prime STAR GXL DNA Polymerase Kit was used to PCR amplify the full length cDNA. The SMARTbell libraries were constructed with the SMARTbell template prep kit. Conduct damage repair and end repair. The stem loop sequencing adaptors were linked to both ends of the DNA fragment and used to remove the failed fragment using exonuclease.     FL-cDNA TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel   SRP438861   assembly:GRCz11 P02TYR22614794_1_r64053_20220510_083113_3_G01.ccs.bam bam 2243456468.0 884312.0 P02TYR22614794 1 r64053 20220510 083113 3 G01.ccs.bam 0:2536.95 A:619660008;C:518127052;G:544711614;T:560957794;N:0 2536       619660008 518127052 544711614 560957794 0 SRX20461637 SRS17774508 SRA1641718 Institute of hydrobiology, chinese academy od sciences|Aquatic Biodiversity and Resource Conservation Res Institute of hydrobiology, chinese academy od sciences 1 0.61172   0.00053   0.84859   0.47684   2357   T   long read pacbio pacbio_modern full_length cdna_unspecified smarter bulk unknown unknown   China 2023-05-21 Zygote Embryo Embryo Imprecise All anatomical structures

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