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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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