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11 rows where experiment.library_selection = "Oligo-dT", experiment.library_source = "TRANSCRIPTOMIC" and experiment.platform = "PACBIO_SMRT"

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devstage_curation 4

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • PACBIO_SMRT · 11 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 11 ✖

experiment.library_selection 1

  • Oligo-dT · 11 ✖

experiment.library_layout 1

devstage_curation_coarse 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

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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");;