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27 rows where devstage_curation = "Zygote" and experiment.library_selection = "Oligo-dT"

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tissue_curation 3

tissue_curation_coarse 2

technology 2

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 27 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Zygote · 27 ✖
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
28569 28569 SRR26395043 SRX22100890 SRS19166016 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 RNA seq rep8   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:SR 1 8|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate8 DR 027 DR 027 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-8_1.fq.gz C1-8_2.fq.gz fastq fastq 14524806800.0 51874310.0 C1 8 1.fq.gz 0:140 1:140 A:3808586515;C:3473203895;G:3505848142;T:3737124558;N:43690 140 140     3808586515 3473203895 3505848142 3737124558 43690 SRX22100890 SRS19166016 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95859 0.96129 0.01726 0.01698 0.85405 0.85374 0.47349 0.47931 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28570 28570 SRR26395044 SRX22100889 SRS19166015 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 RNA seq rep7   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:SR 1 7|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate7 DR 026 DR 026 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-7_1.fq.gz C1-7_2.fq.gz fastq fastq 20478629360.0 73137962.0 C1 7 1.fq.gz 0:140 1:140 A:5376265063;C:4892923429;G:4935127460;T:5274249841;N:63567 140 140     5376265063 4892923429 4935127460 5274249841 63567 SRX22100889 SRS19166015 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95971 0.96278 0.01686 0.01629 0.85411 0.85387 0.45729 0.47652 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28571 28571 SRR26395045 SRX22100888 SRS19166014 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 RNA seq rep6   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:SR 1 6|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate6 DR 025 DR 025 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-6_1.fq.gz C1-6_2.fq.gz fastq fastq 16358886880.0 58424596.0 C1 6 1.fq.gz 0:140 1:140 A:4287038412;C:3917335110;G:3953513580;T:4200950421;N:49357 140 140     4287038412 3917335110 3953513580 4200950421 49357 SRX22100888 SRS19166014 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.96027 0.96304 0.01855 0.01825 0.84271 0.84285 0.47803 0.47354 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28572 28572 SRR26395046 SRX22100887 SRS19166013 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 RNA seq rep5   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:SR 1 5|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate5 DR 024 DR 024 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-5_1.fq.gz C1-5_2.fq.gz fastq fastq 17004986600.0 60732095.0 C1 5 1.fq.gz 0:140 1:140 A:4459128776;C:4070413583;G:4104544139;T:4370848562;N:51540 140 140     4459128776 4070413583 4104544139 4370848562 51540 SRX22100887 SRS19166013 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95691 0.95965 0.01876 0.01822 0.84003 0.83934 0.47976 0.47873 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28573 28573 SRR26395047 SRX22100886 SRS19166012 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 RNA seq rep4   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:SR 1 4|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate4 DR 023 DR 023 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-4_1.fq.gz C1-4_2.fq.gz fastq fastq 17516685480.0 62559591.0 C1 4 1.fq.gz 0:140 1:140 A:4618802699;C:4171295741;G:4210242921;T:4516296296;N:47823 140 140     4618802699 4171295741 4210242921 4516296296 47823 SRX22100886 SRS19166012 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95994 0.96214 0.01942 0.01842 0.8421 0.84157 0.47848 0.47528 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28574 28574 SRR26395048 SRX22100885 SRS19166011 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 RNA seq rep3   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:SR 1 3|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate3 DR 022 DR 022 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-3_1.fq.gz C1-3_2.fq.gz fastq fastq 19515282360.0 69697437.0 C1 3 1.fq.gz 0:140 1:140 A:5115977218;C:4670888345;G:4717977881;T:5010379939;N:58977 140 140     5115977218 4670888345 4717977881 5010379939 58977 SRX22100885 SRS19166011 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95708 0.95865 0.02126 0.02102 0.84246 0.84216 0.46934 0.47058 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28575 28575 SRR26395049 SRX22100884 SRS19166010 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 RNA seq rep2   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:SR 1 2|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate2 DR 021 DR 021 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-2_1.fq.gz C1-2_2.fq.gz fastq fastq 20726034000.0 74021550.0 C1 2 1.fq.gz 0:140 1:140 A:5504115856;C:4899295944;G:4943875721;T:5378685883;N:60596 140 140     5504115856 4899295944 4943875721 5378685883 60596 SRX22100884 SRS19166010 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95721 0.95927 0.0207 0.01959 0.83287 0.8326 0.47491 0.47327 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28577 28577 SRR26395052 SRX22100881 SRS19166007 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 RNA seq rep1   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:SR 1 1|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: 1 cell replicate1 DR 020 DR 020 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C1-1_1.fq.gz C1-1_2.fq.gz fastq fastq 17399401600.0 62140720.0 C1 1 1.fq.gz 0:140 1:140 A:4537529281;C:4191810259;G:4227724301;T:4442283593;N:54166 140 140     4537529281 4191810259 4227724301 4442283593 54166 SRX22100881 SRS19166007 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.9597 0.96271 0.01629 0.01558 0.83909 0.83818 0.46855 0.46911 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28578 28578 SRR26395053 SRX22100880 SRS19166006 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 RNA seq rep8   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:SR 0 8|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate8 DR 019 DR 019 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-8_1.fq.gz C0-8_2.fq.gz fastq fastq 18183625040.0 64941518.0 C0 8 1.fq.gz 0:140 1:140 A:4781555399;C:4337050646;G:4373956478;T:4691007549;N:54968 140 140     4781555399 4337050646 4373956478 4691007549 54968 SRX22100880 SRS19166006 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95834 0.96072 0.01841 0.01795 0.84577 0.84524 0.4829 0.48081 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28579 28579 SRR26395054 SRX22100879 SRS19166005 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 RNA seq rep7   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:SR 0 7|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate7 DR 018 DR 018 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-7_1.fq.gz C0-7_2.fq.gz fastq fastq 15161389040.0 54147818.0 C0 7 1.fq.gz 0:140 1:140 A:3994107417;C:3609023200;G:3642319126;T:3915893474;N:45823 140 140     3994107417 3609023200 3642319126 3915893474 45823 SRX22100879 SRS19166005 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95744 0.95996 0.01875 0.01807 0.83725 0.83694 0.47055 0.46748 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28580 28580 SRR26395055 SRX22100878 SRS19166004 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 RNA seq rep6   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:SR 0 6|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate6 DR 017 DR 017 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-6_2.fq.gz C0-6_1.fq.gz fastq fastq 18372330760.0 65615467.0 C0 6 1.fq.gz 0:140 1:140 A:4848831784;C:4365620714;G:4403697790;T:4754124527;N:55945 140 140     4848831784 4365620714 4403697790 4754124527 55945 SRX22100878 SRS19166004 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.96339 0.96549 0.01832 0.01765 0.84719 0.84699 0.47322 0.48081 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28581 28581 SRR26395056 SRX22100877 SRS19166003 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 RNA seq rep5   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:SR 0 5|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate5 DR 016 DR 016 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-5_1.fq.gz C0-5_2.fq.gz fastq fastq 17733025240.0 63332233.0 C0 5 1.fq.gz 0:140 1:140 A:4656835082;C:4237633580;G:4277583056;T:4560919266;N:54256 140 140     4656835082 4237633580 4277583056 4560919266 54256 SRX22100877 SRS19166003 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95837 0.95974 0.01811 0.01704 0.85242 0.85184 0.4749 0.47361 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28582 28582 SRR26395057 SRX22100876 SRS19166002 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 RNA seq rep4   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:SR 0 4|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate4 DR 015 DR 015 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-4_1.fq.gz C0-4_2.fq.gz fastq fastq 17317453440.0 61848048.0 C0 4 1.fq.gz 0:140 1:140 A:4549082241;C:4110729602;G:4198645748;T:4458943221;N:52628 140 140     4549082241 4110729602 4198645748 4458943221 52628 SRX22100876 SRS19166002 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.9524 0.95183 0.0196 0.01909 0.84443 0.84429 0.47269 0.47317 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28583 28583 SRR26395058 SRX22100875 SRS19166001 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 RNA seq rep3   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:SR 0 3|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate3 DR 014 DR 014 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-3_1.fq.gz C0-3_2.fq.gz fastq fastq 20285193040.0 72447118.0 C0 3 1.fq.gz 0:140 1:140 A:5333425678;C:4804605480;G:4928569454;T:5218530436;N:61992 140 140     5333425678 4804605480 4928569454 5218530436 61992 SRX22100875 SRS19166001 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95386 0.95151 0.0188 0.01789 0.84226 0.8424 0.48241 0.47074 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28584 28584 SRR26395059 SRX22100874 SRS19166000 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 RNA seq rep2   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:SR 0 2|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate2 DR 013 DR 013 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-2_1.fq.gz C0-2_2.fq.gz fastq fastq 18750583600.0 66966370.0 C0 2 1.fq.gz 0:140 1:140 A:4964845916;C:4440076965;G:4485931411;T:4859670521;N:58787 140 140     4964845916 4440076965 4485931411 4859670521 58787 SRX22100874 SRS19166000 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95711 0.95855 0.02082 0.01977 0.83733 0.83792 0.4711 0.47348 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote Embryo Embryo Imprecise All anatomical structures
28585 28585 SRR26395060 SRX22100873 SRS19165999 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 RNA seq rep1   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:SR 0 1|BioSampleModel:Model organism or animal                 Illumina RNA seq of zebrafish: fertilized egg replicate1 DR 012 DR 012 mRNA from five stages fertilized egg 1 cell 64 cell 1k cell and shield was extracted with Dynabeads@ mRNA Purification Kit Ambion and subjected to TURBOTM DNase lnvitrogen treatment. RNA Seq libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina NEB USA and then sequenced at 275 bp paired end mode on an Illumina HiSeq X Ten system with 8 replicates for each stage.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA HiSeq X Ten   SRP466518     C0-1_1.fq.gz C0-1_2.fq.gz fastq fastq 15875566560.0 56698452.0 C0 1 1.fq.gz 0:140 1:140 A:4193265882;C:3760934849;G:3804966904;T:4116350955;N:47970 140 140     4193265882 3760934849 3804966904 4116350955 47970 SRX22100873 SRS19165999 SRA1731898 University of Michigan|Computational Medicine and Bioinformatics University of Michigan 2 0.95661 0.9602 0.02103 0.02033 0.84129 0.84092 0.48083 0.47857 140 140 B B biological fallback assumption illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   United States 2023-10-16 Zygote 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
61762 61762 SRR13015620 SRX9466616 SRS7678764 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 2 0hpf.rep2   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep2 lane2 PJ KH 004 2 PJ KH 004 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_004_S4_L002_R1_001.fastq.gz PJ_KH_004_S4_L002_R2_001.fastq.gz fastq fastq 6747035756.0 22341178.0 PJ KH 004 S4 L002 R1 001.fastq.gz 0:151 1:151 A:1749259364;C:1630082050;G:1671975335;T:1694420838;N:1298169 151 151     1749259364 1630082050 1671975335 1694420838 1298169 SRX9466616 SRS7678764 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.91606 0.915 0.0228 0.02253 0.8462 0.84764 0.47581 0.47811 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61763 61763 SRR13015621 SRX9466615 SRS7678764 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 2 0hpf.rep2   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep2 lane1 PJ KH 004 1 PJ KH 004 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_004_S4_L001_R1_001.fastq.gz PJ_KH_004_S4_L001_R2_001.fastq.gz fastq fastq 7002326926.0 23186513.0 PJ KH 004 S4 L001 R1 001.fastq.gz 0:151 1:151 A:1813808137;C:1692625163;G:1737142909;T:1756973437;N:1777280 151 151     1813808137 1692625163 1737142909 1756973437 1777280 SRX9466615 SRS7678764 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.91797 0.91431 0.02335 0.02297 0.84682 0.84867 0.48058 0.47562 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61764 61764 SRR13015622 SRX9466614 SRS7678763 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 2 0hpf.rep1   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep1 lane2 PJ KH 003 2 PJ KH 003 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_003_S3_L002_R1_001.fastq.gz PJ_KH_003_S3_L002_R2_001.fastq.gz fastq fastq 6323928622.0 20940161.0 PJ KH 003 S3 L002 R1 001.fastq.gz 0:151 1:151 A:1664173214;C:1500258415;G:1538972894;T:1619319465;N:1204634 151 151     1664173214 1500258415 1538972894 1619319465 1204634 SRX9466614 SRS7678763 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.91771 0.91711 0.02141 0.02071 0.84382 0.84632 0.4721 0.47896 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61766 61766 SRR13015624 SRX9466612 SRS7678763 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 2 0hpf.rep1   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 2|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 2 Rep1 lane1 PJ KH 003 1 PJ KH 003 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_003_S3_L001_R1_001.fastq.gz PJ_KH_003_S3_L001_R2_001.fastq.gz fastq fastq 6652658038.0 22028669.0 PJ KH 003 S3 L001 R1 001.fastq.gz 0:151 1:151 A:1748718497;C:1579368495;G:1621147905;T:1701739850;N:1683291 151 151     1748718497 1579368495 1621147905 1701739850 1683291 SRX9466612 SRS7678763 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.91835 0.91483 0.02199 0.02155 0.84262 0.84471 0.4828 0.4803 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61767 61767 SRR13015625 SRX9466611 SRS7678761 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 1 0hpf.rep2   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep2 lane2 PJ KH 002 2 PJ KH 002 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_002_S2_L002_R1_001.fastq.gz PJ_KH_002_S2_L002_R2_001.fastq.gz fastq fastq 7116731170.0 23565335.0 PJ KH 002 S2 L002 R1 001.fastq.gz 0:151 1:151 A:1813322250;C:1745818869;G:1791244865;T:1764990020;N:1355166 151 151     1813322250 1745818869 1791244865 1764990020 1355166 SRX9466611 SRS7678761 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.90942 0.90881 0.01338 0.01286 0.83512 0.8365 0.47569 0.47472 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61768 61768 SRR13015626 SRX9466610 SRS7678761 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 1 0hpf.rep2   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 2|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep2 lane1 PJ KH 002 1 PJ KH 002 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_002_S2_L001_R1_001.fastq.gz PJ_KH_002_S2_L001_R2_001.fastq.gz fastq fastq 7285422632.0 24123916.0 PJ KH 002 S2 L001 R1 001.fastq.gz 0:151 1:151 A:1854975023;C:1787715446;G:1835538323;T:1805336454;N:1857386 151 151     1854975023 1787715446 1835538323 1805336454 1857386 SRX9466610 SRS7678761 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.90695 0.90384 0.01372 0.01325 0.83644 0.83806 0.48376 0.46874 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61769 61769 SRR13015627 SRX9466609 SRS7678760 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 1 0hpf.rep1   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep1 lane2 PJ KH 001 2 PJ KH 001 2 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_001_S1_L002_R1_001.fastq.gz PJ_KH_001_S1_L002_R2_001.fastq.gz fastq fastq 5744360120.0 19021060.0 PJ KH 001 S1 L002 R1 001.fastq.gz 0:151 1:151 A:1471481677;C:1411353282;G:1443418761;T:1417001880;N:1104520 151 151     1471481677 1411353282 1443418761 1417001880 1104520 SRX9466609 SRS7678760 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.78051 0.78166 0.02032 0.0196 0.84378 0.84563 0.51089 0.51533 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
61770 61770 SRR13015628 SRX9466608 SRS7678760 SRP291905 PRJNA674002 A to I RNA editing in zebrafish during development PRJNA674002 Other Here we investigated A to I RNA editing in early zebrafish development and in the adult brain. Raw unmapped sequencing output from stranded mRNA libraries can be found under this accession.       zebrafish embryos 0 hpf single cross 1 0hpf.rep1   strain:AB wildtype|dev stage:0 hpf|sex:unknown|tissue:whole embryo|embryos derived by cross:single cross 1|biological replicate:replicate 1|assay type:mRNA seq|BioSampleModel:Model organism or animal                 mRNA seq of whole zebrafish embryos wildtype AB 0 hpf single cross 1 Rep1 lane1 PJ KH 001 1 PJ KH 001 1 stranded mRNA     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   SRP291905     PJ_KH_001_S1_L001_R1_001.fastq.gz PJ_KH_001_S1_L001_R2_001.fastq.gz fastq fastq 6028405314.0 19961607.0 PJ KH 001 S1 L001 R1 001.fastq.gz 0:151 1:151 A:1542966381;C:1481961666;G:1516533761;T:1485424027;N:1519479 151 151     1542966381 1481961666 1516533761 1485424027 1519479 SRX9466608 SRS7678760 SRA1153075 MDC Berlin|BIMSB MDC Berlin 2 0.78061 0.77898 0.02018 0.01968 0.84508 0.84654 0.52141 0.51846 151 151 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Germany 2020-11-10 Zygote Embryo Whole Organism All anatomical structures
75608 75608 SRR24742192 SRX20519420 SRS17829368 SRP439656 PRJNA975724 Key factors in the process of biliary epithelial cells to bipotential progenitor cells dedifferentiation PRJNA975724 Other Uncover the regulatory mechanisms underlying biliary cell dedifferentiation.     The fish were treated with mtz at 5 dpf and then the livers were collected post 24 hours treatment namly regeneration 0 hour. scRNA seq of zebrafish R0h livers Livers of lfabp:Dendra2 NTR fish at mtz R0h   strain:ABGO|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:mtz R0h|sex:pooled male and female|tissue:liver|birth location:China|collection date:2021 04 29|geo loc name:China: Chongqing|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish R0h livers 20210429 S3 R0 20210429 S3 R0 Using Chromium Single cell three prime GEM v3.1 Reagent kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439656     R21049148-20210429-S3-R0-1_combined_R1.fastq.gz R21049148-20210429-S3-R0-1_combined_R2.fastq.gz R21049148-20210429-S3-R0-2_combined_R1.fastq.gz R21049148-20210429-S3-R0-2_combined_R2.fastq.gz R21049148-20210429-S3-R0-3_combined_R1.fastq.gz R21049148-20210429-S3-R0-3_combined_R2.fastq.gz R21049148-20210429-S3-R0-4_combined_R1.fastq.gz R21049148-20210429-S3-R0-4_combined_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq 108860887800.0 362869626.0 R21049148 20210429 S3 R0 1 combined R1.fastq.gz 0:150 1:150 A:46078842047;C:20145501988;G:19787836142;T:22846772612;N:1935011 150 150     46078842047 20145501988 19787836142 22846772612 1935011 SRX20519420 SRS17829368 SRA1643264 Institute of Developmental Biology and Regenerative Medicine|Southwest University Institute of Developmental Biology and Regenerative Medicine AccuraMed Company 2 0.0 0.92113 0.0 0.15798 1.0 0.81215   0.58532 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-05-25 Zygote Embryo Liver Liver and Biliary System

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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");;