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run_metadata

10 rows where devstage_curation = "Blastula" and experiment.platform = "PACBIO_SMRT"

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experiment.library_strategy 2

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • PACBIO_SMRT · 10 ✖

experiment.library_source 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 10 ✖
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
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
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

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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");;