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21 rows where devstage_curation = "Zygote" and experiment.platform = "PACBIO_SMRT"

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tissue_curation 3

experiment.library_selection 3

experiment.library_strategy 2

technology 1

experiment.platform 1

  • PACBIO_SMRT · 21 ✖

experiment.library_source 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Zygote · 21 ✖
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
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
34978 34978 SRR32588735 SRX27895216 SRS24266218 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from embryo zero hpf C2 F2 0   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 0 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal                 Iso Seq RNA from embyo 0 hpf C2 F2 0 C2 F2 0 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m54313U_231110_180503.hifi_reads.flnc.fastq.gz fastq 8144050440.0 3744842.0 m54313U 231110 180503.hifi reads.flnc.fastq.gz 0:2174.74 A:2267401658;C:1836982566;G:1935470734;T:2104195482;N:0 2174       2267401658 1836982566 1935470734 2104195482 0 SRX27895216 SRS24266218 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute 1 0.76793   0.00473   0.80371   0.50925   1489   T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Zygote Embryo Muscle Muscular System
50511 50511 SRR8293425 SRX5108028 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 2 3K D03 1 2 3K D03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160828_125709_42199_c101055502550000001823247601061763_s1_p0.1.bax.h5 m160828_125709_42199_c101055502550000001823247601061763_s1_p0.2.bax.h5 m160828_125709_42199_c101055502550000001823247601061763_s1_p0.3.bax.h5 m160828_125709_42199_c101055502550000001823247601061763_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3189114337.0 163482.0 2 3K D03 1.tar.gz   A:1019691460;C:775938787;G:628460211;T:736274173;N:0         1019691460 775938787 628460211 736274173 0 SRX5108028 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50512 50512 SRR8293426 SRX5108027 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 2 3K E03 1 2 3K E03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160828_171546_42199_c101055502550000001823247601061764_s1_p0.1.bax.h5 m160828_171546_42199_c101055502550000001823247601061764_s1_p0.2.bax.h5 m160828_171546_42199_c101055502550000001823247601061764_s1_p0.3.bax.h5 m160828_171546_42199_c101055502550000001823247601061764_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3603145484.0 163482.0 2 3K E03 1.tar.gz   A:1041332538;C:789941375;G:785608794;T:952634306;N:0         1041332538 789941375 785608794 952634306 0 SRX5108027 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50513 50513 SRR8293427 SRX5108026 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 1 2K D05 1 1 2K D05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160831_064528_42199_c101016682550000001823228410211623_s1_p0.1.bax.h5 m160831_064528_42199_c101016682550000001823228410211623_s1_p0.2.bax.h5 m160831_064528_42199_c101016682550000001823228410211623_s1_p0.3.bax.h5 m160831_064528_42199_c101016682550000001823228410211623_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 4494598972.0 163482.0 1 2K D05 1.tar.gz   A:1263523570;C:919488657;G:1005901638;T:1241749988;N:0         1263523570 919488657 1005901638 1241749988 0 SRX5108026 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50514 50514 SRR8293428 SRX5108025 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 1 2K E05 1 1 2K E05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160831_110725_42199_c101016682550000001823228410211624_s1_p0.1.bax.h5 m160831_110725_42199_c101016682550000001823228410211624_s1_p0.2.bax.h5 m160831_110725_42199_c101016682550000001823228410211624_s1_p0.3.bax.h5 m160831_110725_42199_c101016682550000001823228410211624_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 4610281055.0 163482.0 1 2K E05 1.tar.gz   A:1313884618;C:971754386;G:994748647;T:1264950574;N:0         1313884618 971754386 994748647 1264950574 0 SRX5108025 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50515 50515 SRR8293429 SRX5108024 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 1 2K F03 1 1 2K F03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160828_213458_42199_c101055502550000001823247601061765_s1_p0.1.bax.h5 m160828_213458_42199_c101055502550000001823247601061765_s1_p0.2.bax.h5 m160828_213458_42199_c101055502550000001823247601061765_s1_p0.3.bax.h5 m160828_213458_42199_c101055502550000001823247601061765_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 6488051235.0 163482.0 1 2K F03 1.tar.gz   A:1835535517;C:1366315971;G:1464006715;T:1752025312;N:0         1835535517 1366315971 1464006715 1752025312 0 SRX5108024 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50516 50516 SRR8293430 SRX5108023 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 1 2K G05 1 1 2K G05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160829_020016_42199_c101055502550000001823247601061766_s1_p0.1.bax.h5 m160829_020016_42199_c101055502550000001823247601061766_s1_p0.2.bax.h5 m160829_020016_42199_c101055502550000001823247601061766_s1_p0.3.bax.h5 m160829_020016_42199_c101055502550000001823247601061766_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 6326394753.0 163482.0 1 2K G03 1.tar.gz   A:1844148357;C:1410947877;G:1367704673;T:1640545786;N:0         1844148357 1410947877 1367704673 1640545786 0 SRX5108023 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50517 50517 SRR8293431 SRX5108022 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 0.5 1K E03 1 0.5 1K E03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160921_142928_42199_c100979762550000001823212907061657_s1_X0.bas.h5 m160921_142928_42199_c100979762550000001823212907061657_s1_X0.3.bax.h5 m160921_142928_42199_c100979762550000001823212907061657_s1_X0.2.bax.h5 m160921_142928_42199_c100979762550000001823212907061657_s1_X0.1.bax.h5 pacbio_native pacbio_native pacbio_native pacbio_native 1906153604.0 163482.0 0.5 1K E03 1.tar.gz   A:568523342;C:407560314;G:389613623;T:500427928;N:0         568523342 407560314 389613623 500427928 0 SRX5108022 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-08 Zygote Embryo Gonad Reproductive System
50518 50518 SRR8293432 SRX5108021 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 0.5 1K F03 1 0.5 1K F03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160921_184841_42199_c101055652550000001823238312291647_s1_p0.1.bax.h5 m160921_184841_42199_c101055652550000001823238312291647_s1_p0.2.bax.h5 m160921_184841_42199_c101055652550000001823238312291647_s1_p0.3.bax.h5 m160921_184841_42199_c101055652550000001823238312291647_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 4156910909.0 163482.0 0.5 1K F03 1.tar.gz   A:1183616929;C:878682771;G:890537851;T:1136413189;N:0         1183616929 878682771 890537851 1136413189 0 SRX5108021 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50519 50519 SRR8293433 SRX5108020 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 0.5 1K G03 1 0.5 1K G03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160829_063211_42199_c101055502550000001823247601061767_s1_p0.bas.h5 m160829_063211_42199_c101055502550000001823247601061767_s1_p0.3.bax.h5 m160829_063211_42199_c101055502550000001823247601061767_s1_p0.2.bax.h5 m160829_063211_42199_c101055502550000001823247601061767_s1_p0.1.bax.h5 pacbio_native pacbio_native pacbio_native pacbio_native 5660530911.0 163482.0 0.5 1K H03 1.tar.gz   A:1835439052;C:1406954743;G:1037776936;T:1307349158;N:0         1835439052 1406954743 1037776936 1307349158 0 SRX5108020 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-08 Zygote Embryo Gonad Reproductive System
50520 50520 SRR8293434 SRX5108019 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 1 2K C05 1 1 2K C05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160831_022615_42199_c101016682550000001823228410211622_s1_p0.1.bax.h5 m160831_022615_42199_c101016682550000001823228410211622_s1_p0.2.bax.h5 m160831_022615_42199_c101016682550000001823228410211622_s1_p0.3.bax.h5 m160831_022615_42199_c101016682550000001823228410211622_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3047073997.0 163482.0 1 2K C05 1.tar.gz   A:862003813;C:632482019;G:660595007;T:843966997;N:0         862003813 632482019 660595007 843966997 0 SRX5108019 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50521 50521 SRR8293435 SRX5108018 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 2 3K F05 1 2 3K F05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160831_152721_42199_c101016682550000001823228410211625_s1_p0.1.bax.h5 m160831_152721_42199_c101016682550000001823228410211625_s1_p0.2.bax.h5 m160831_152721_42199_c101016682550000001823228410211625_s1_p0.3.bax.h5 m160831_152721_42199_c101016682550000001823228410211625_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3504827488.0 163482.0 2 3K F05 1.tar.gz   A:1035191904;C:787763869;G:735456262;T:916015813;N:0         1035191904 787763869 735456262 916015813 0 SRX5108018 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50522 50522 SRR8293436 SRX5108017 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 2 3K G05 1 2 3K G05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160831_195005_42199_c101016682550000001823228410211626_s1_p0.1.bax.h5 m160831_195005_42199_c101016682550000001823228410211626_s1_p0.2.bax.h5 m160831_195005_42199_c101016682550000001823228410211626_s1_p0.3.bax.h5 m160831_195005_42199_c101016682550000001823228410211626_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3325636539.0 163482.0 2 3K G05 1.tar.gz   A:945624516;C:712334057;G:726829680;T:910995593;N:0         945624516 712334057 726829680 910995593 0 SRX5108017 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50523 50523 SRR8293437 SRX5108016 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 2 3K H05 1 2 3K H05 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160901_000924_42199_c101016682550000001823228410211627_s1_p0.1.bax.h5 m160901_000924_42199_c101016682550000001823228410211627_s1_p0.2.bax.h5 m160901_000924_42199_c101016682550000001823228410211627_s1_p0.3.bax.h5 m160901_000924_42199_c101016682550000001823228410211627_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 3219471171.0 163482.0 2 3K H05 1.tar.gz   A:955121582;C:717645710;G:671893655;T:846270302;N:0         955121582 717645710 671893655 846270302 0 SRX5108016 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50524 50524 SRR8293438 SRX5108015 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 3K plus C03 1 3K plus C03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160828_083719_42199_c101055502550000001823247601061762_s1_p0.1.bax.h5 m160828_083719_42199_c101055502550000001823247601061762_s1_p0.2.bax.h5 m160828_083719_42199_c101055502550000001823247601061762_s1_p0.3.bax.h5 m160828_083719_42199_c101055502550000001823247601061762_s1_p0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 2241335194.0 163482.0 3K plus C03 1.tar.gz   A:714450646;C:554512788;G:442348736;T:513624736;N:0         714450646 554512788 442348736 513624736 0 SRX5108015 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50525 50525 SRR8293439 SRX5108014 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 3K plus G03 1 3K plus G03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160921_231100_42199_c100829932550000001823181912311557_s1_X0.1.bax.h5 m160921_231100_42199_c100829932550000001823181912311557_s1_X0.2.bax.h5 m160921_231100_42199_c100829932550000001823181912311557_s1_X0.3.bax.h5 m160921_231100_42199_c100829932550000001823181912311557_s1_X0.bas.h5 pacbio_native pacbio_native pacbio_native pacbio_native 1500621674.0 163482.0 3K plus G03 1.tar.gz   A:461686513;C:353289117;G:298838025;T:376337789;N:0         461686513 353289117 298838025 376337789 0 SRX5108014 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-10 Zygote Embryo Gonad Reproductive System
50526 50526 SRR8293440 SRX5108013 SRS4117494 SRP172911 PRJNA498365 Raw sequence reads in the unfertilized eggs of zebrafish Danio rerio PRJNA498365 Other Raw sequence reads of full length transcriptome sequencing in the unfertilized eggs of zebrafish Danio rerio.     Three female zebrafish were selected and 100 unfertilized eggs from each female were harvested as three samples Z1 1 Z1 2 and Z1 3 respectively; Identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M. Model organism or animal sample from Danio rerio unfertilized eggs from three female zebrafish were harvested as samples Z1 M   isolate:3 female zebrafish were selected and 100 unfertilized eggs from each female were harvested as 3 samples Z1 1 Z1 2 and Z1 3 respectively; and identical quantities of RNA from Z1 1 Z1 2 and Z1 3 were combined into sample Z1 M.|dev stage:unfertilized egg|sex:female|tissue:ovary|BioSampleModel:Model organism or animal                 Full length transcriptome sequencing of zebrafish Danio rerio : adult female unfertilized eggs. 3K plus H03 1 3K plus H03 1 RNA sample Z1 M was reverse transcribed into cDNA. Four fragment ranges 0.5 1K 1 2K 2 3K and >3K were prepared according to the PacBio Iso Seq protocol. PacBio RS II sequencing reactions of 16 SMRT single molecule real time cells 3 cells of 0.5 1K 5 cells of 1 2K 5 cells of 2 3K 3 cells of >3K were performed in DNA Sequencing Reagent 4.0 Clontech Mountain View California USA.     RNA-Seq TRANSCRIPTOMIC RANDOM PCR SINGLE PACBIO_SMRT PacBio RS II   SRP172911     m160922_033036_42199_c101055332550000001823238312291650_s1_p0.bas.h5 m160922_033036_42199_c101055332550000001823238312291650_s1_p0.3.bax.h5 m160922_033036_42199_c101055332550000001823238312291650_s1_p0.2.bax.h5 m160922_033036_42199_c101055332550000001823238312291650_s1_p0.1.bax.h5 pacbio_native pacbio_native pacbio_native pacbio_native 2783940881.0 163482.0 3K plus H03 1.tar.gz   A:785688594;C:616582821;G:618500268;T:743803835;N:0         785688594 616582821 618500268 743803835 0 SRX5108013 SRS4117494 SRA820074 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences                             pacbio pacbio_early full_length random_priming unknown bulk unknown unknown   China 2018-12-08 Zygote Embryo Gonad Reproductive System
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");;