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330 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RT-PCR" and experiment.library_strategy = "RNA-Seq"

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tissue_curation >10

devstage_curation 9

devstage_curation_coarse 6

technology 2

experiment.library_source 2

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 330 ✖

experiment.library_selection 1

  • RT-PCR · 330 ✖

experiment.library_layout 1

  • PAIRED · 330 ✖
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
30716 30716 SRR28342048 SRX23948605 SRS20750294 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B3 3xflag RESA CLIP input B3 AGN003279   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002510|replicate ref:AGN003279|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 input|replicate label short:RESA CLIP Upf1 #3737 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B3 AGR004059 AGR004059 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004059_R1.fastq AGR004059_R2.fastq fastq fastq 15446715026.0 51148063.0 AGR004059 R1.fastq.zst 0:151 1:151 A:4298384942;C:3080575022;G:4004069877;T:4063619821;N:65364 151 151     4298384942 3080575022 4004069877 4063619821 65364 SRX23948605 SRS20750294 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30717 30717 SRR28342039 SRX23948614 SRS20750302 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 R843C RESA HITS CLIP B1 3xflag upf1 R843C RESA HITS CLIP B1 AGN003273   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003273|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 R843C RESA HITS CLIP B1 AGR004053 AGR004053 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004053_R1.fastq AGR004053_R2.fastq fastq fastq 10545264992.0 34918096.0 AGR004053 R1.fastq.zst 0:151 1:151 A:2943441620;C:2155828506;G:2709854276;T:2736095568;N:45022 151 151     2943441620 2155828506 2709854276 2736095568 45022 SRX23948614 SRS20750302 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30718 30718 SRR28342040 SRX23948613 SRS20750303 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 C126S RESA HITS CLIP B2 3xflag upf1 C126S RESA HITS CLIP B2 AGN003282   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003282|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 C126S RESA HITS CLIP B2 AGR004062 AGR004062 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004062_R1.fastq AGR004062_R2.fastq fastq fastq 11134300590.0 36868545.0 AGR004062 R1.fastq.zst 0:151 1:151 A:3063023630;C:2386509106;G:2925940275;T:2758782993;N:44586 151 151     3063023630 2386509106 2925940275 2758782993 44586 SRX23948613 SRS20750303 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30719 30719 SRR28342041 SRX23948612 SRS20750301 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 C126S RESA HITS CLIP B1 3xflag upf1 C126S RESA HITS CLIP B1 AGN003281   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003281|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 C126S RESA HITS CLIP B1 AGR004061 AGR004061 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004061_R1.fastq AGR004061_R2.fastq fastq fastq 13368435586.0 44266343.0 AGR004061 R1.fastq.zst 0:151 1:151 A:3603822055;C:2659540495;G:3591989409;T:3513026539;N:57088 151 151     3603822055 2659540495 3591989409 3513026539 57088 SRX23948612 SRS20750301 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30720 30720 SRR28342042 SRX23948611 SRS20750300 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 G495R/G497E RESA HITS CLIP B2 3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGN003278   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003278|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGR004058 AGR004058 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004058_R1.fastq AGR004058_R2.fastq fastq fastq 13750586084.0 45531742.0 AGR004058 R1.fastq.zst 0:151 1:151 A:3775460380;C:2748834924;G:3672092546;T:3554141983;N:56251 151 151     3775460380 2748834924 3672092546 3554141983 56251 SRX23948611 SRS20750300 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30721 30721 SRR28342043 SRX23948610 SRS20750299 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 G495R/G497E RESA HITS CLIP B1 3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGN003277   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003277|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGR004057 AGR004057 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004057_R1.fastq AGR004057_R2.fastq fastq fastq 10708529212.0 35458706.0 AGR004057 R1.fastq.zst 0:151 1:151 A:2983511099;C:2231542625;G:2842811089;T:2650619142;N:45257 151 151     2983511099 2231542625 2842811089 2650619142 45257 SRX23948610 SRS20750299 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30722 30722 SRR28342044 SRX23948609 SRS20750297 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag gfp RESA HITS CLIP B1 3xflag gfp RESA HITS CLIP B1 AGN002579   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001970|replicate ref:AGN002579|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:gfp CLIP|replicate label short:gfp CLIP B1|BioSampleModel:Model organism or animal                 3xflag gfp RESA HITS CLIP B1 AGR003308 AGR003308 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003308_R1.fastq AGR003308_R2.fastq fastq fastq 507167460.0 2510730.0 AGR003308 R1.fastq.zst 0:101 1:101 A:156207937;C:97169427;G:111291367;T:142479104;N:19625 101 101     156207937 97169427 111291367 142479104 19625 SRX23948609 SRS20750297 SRA1824033 Yale University|Genetics Yale University                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30723 30723 SRR28342045 SRX23948608 SRS20750298 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA HITS CLIP input B4 3xflag RESA CLIP input B4 AGN003267   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002504|replicate ref:AGN003267|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 input|replicate label short:RESA CLIP Upf1 #3650 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B4 AGR004047 AGR004047 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004047_R2.fastq AGR004047_R1.fastq fastq fastq 19396379142.0 64226421.0 AGR004047 R1.fastq.zst 0:151 1:151 A:5606633601;C:3872715770;G:4910603410;T:5006345083;N:81278 151 151     5606633601 3872715770 4910603410 5006345083 81278 SRX23948608 SRS20750298 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30724 30724 SRR28342046 SRX23948607 SRS20750295 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3b RESA HITS CLIP B2 3xflag upf3b RESA HITS CLIP B2 AGN002796   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002796|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf3b RESA HITS CLIP B2 AGR003554 AGR003554 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003554_R1.fastq AGR003554_R2.fastq fastq fastq 9047261244.0 44788422.0 AGR003554 R1.fastq.zst 0:101 1:101 A:2711585737;C:1825740983;G:2076537283;T:2433050799;N:346442 101 101     2711585737 1825740983 2076537283 2433050799 346442 SRX23948607 SRS20750295 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30725 30725 SRR28342047 SRX23948606 SRS20750296 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3b RESA HITS CLIP B1 3xflag upf3b RESA HITS CLIP B1 AGN002795   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002795|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf3b RESA HITS CLIP B1 AGR003549 AGR003549 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003549_R1.fastq AGR003549_R2.fastq fastq fastq 9617196770.0 47609885.0 AGR003549 R1.fastq.zst 0:101 1:101 A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990 101 101     2856263963 1963091501 2218118010 2579364306 358990 SRX23948606 SRS20750296 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30726 30726 SRR28342049 SRX23948604 SRS20750292 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3a RESA HITS CLIP B2 3xflag upf3a RESA HITS CLIP B2 AGN002792   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002792|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf3a RESA HITS CLIP B2 AGR003566 AGR003566 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003566_R1.fastq AGR003566_R2.fastq fastq fastq 50318544410.0 249101705.0 AGR003566 R1.fastq.zst 0:101 1:101 A:14930547705;C:10295739682;G:11624332741;T:13466693890;N:1230392 101 101     14930547705 10295739682 11624332741 13466693890 1230392 SRX23948604 SRS20750292 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30727 30727 SRR28342050 SRX23948603 SRS20750293 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3a RESA HITS CLIP B1 3xflag upf3a RESA HITS CLIP B1 AGN002791   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002791|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf3a RESA HITS CLIP B1 AGR003545 AGR003545 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003545_R1.fastq AGR003545_R2.fastq fastq fastq 10770959564.0 53321582.0 AGR003545 R1.fastq.zst 0:101 1:101 A:3207646854;C:2186852059;G:2481889724;T:2894165865;N:405062 101 101     3207646854 2186852059 2481889724 2894165865 405062 SRX23948603 SRS20750293 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30728 30728 SRR28342051 SRX23948602 SRS20750291 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf2 RESA HITS CLIP B2 3xflag upf2 RESA HITS CLIP B2 AGN002788   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002788|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf2 RESA HITS CLIP B2 AGR003541 AGR003541 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003541_R1.fastq AGR003541_R2.fastq fastq fastq 9471117440.0 46886720.0 AGR003541 R1.fastq.zst 0:101 1:101 A:2852420143;C:1898246719;G:2136843599;T:2583254674;N:352305 101 101     2852420143 1898246719 2136843599 2583254674 352305 SRX23948602 SRS20750291 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30729 30729 SRR28342052 SRX23948601 SRS20750290 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf2 RESA HITS CLIP B1 3xflag upf2 RESA HITS CLIP B1 AGN002787   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002787|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf2 RESA HITS CLIP B1 AGR003542 AGR003542 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003542_R1.fastq AGR003542_R2.fastq fastq fastq 10845546044.0 53690822.0 AGR003542 R1.fastq.zst 0:101 1:101 A:3277705832;C:2154122837;G:2449408891;T:2963913264;N:395220 101 101     3277705832 2154122837 2449408891 2963913264 395220 SRX23948601 SRS20750290 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30730 30730 SRR28342053 SRX23948600 SRS20750289 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B5 3xflag upf1 RESA HITS CLIP B5 AGN003270   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003270|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B5 AGR004050 AGR004050 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004050_R1.fastq AGR004050_R2.fastq fastq fastq 11823214534.0 39149717.0 AGR004050 R1.fastq.zst 0:151 1:151 A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480 151 151     3184473505 2558650081 3236214151 2843828317 48480 SRX23948600 SRS20750289 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30731 30731 SRR28342054 SRX23948599 SRS20750288 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B4 3xflag upf1 RESA HITS CLIP B4 AGN003269   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003269|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B4 AGR004049 AGR004049 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004049_R1.fastq AGR004049_R2.fastq fastq fastq 14371221754.0 47586827.0 AGR004049 R1.fastq.zst 0:151 1:151 A:3983698498;C:2912453835;G:3805806498;T:3669203887;N:59036 151 151     3983698498 2912453835 3805806498 3669203887 59036 SRX23948599 SRS20750288 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30732 30732 SRR28342055 SRX23948598 SRS20750287 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B3 3xflag upf1 RESA HITS CLIP B3 AGN002798   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002798|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B3 AGR003555 AGR003555 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003555_R1.fastq AGR003555_R2.fastq fastq fastq 13605076932.0 67351866.0 AGR003555 R1.fastq.zst 0:101 1:101 A:3996372048;C:2823464384;G:3156030119;T:3628752419;N:457962 101 101     3996372048 2823464384 3156030119 3628752419 457962 SRX23948598 SRS20750287 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30733 30733 SRR28342056 SRX23948597 SRS20750283 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B2 3xflag upf1 RESA HITS CLIP B2 AGN002784   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002784|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B2 AGR003552 AGR003552 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003552_R1.fastq AGR003552_R2.fastq fastq fastq 10762870878.0 53281539.0 AGR003552 R1.fastq.zst 0:101 1:101 A:3170047840;C:2223795927;G:2504911576;T:2863700088;N:415447 101 101     3170047840 2223795927 2504911576 2863700088 415447 SRX23948597 SRS20750283 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30734 30734 SRR28342057 SRX23948596 SRS20750286 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B1 3xflag upf1 RESA HITS CLIP B1 AGN002577   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001968|replicate ref:AGN002577|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:upf1 CLIP|replicate label short:upf1 CLIP B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B1 AGR003306 AGR003306 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003306_R1.fastq AGR003306_R2.fastq fastq fastq 529433718.0 2620959.0 AGR003306 R1.fastq.zst 0:101 1:101 A:157881697;C:106579975;G:122214915;T:142736640;N:20491 101 101     157881697 106579975 122214915 142736640 20491 SRX23948596 SRS20750286 SRA1824033 Yale University|Genetics Yale University                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30735 30735 SRR28342058 SRX23948595 SRS20750284 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 R843C RESA HITS CLIP B2 3xflag upf1 R843C RESA HITS CLIP B2 AGN003274   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003274|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 R843C RESA HITS CLIP B2 AGR004054 AGR004054 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004054_R1.fastq AGR004054_R2.fastq fastq fastq 12067359790.0 39958145.0 AGR004054 R1.fastq.zst 0:151 1:151 A:3301899297;C:2532414363;G:3161463027;T:3071532640;N:50463 151 151     3301899297 2532414363 3161463027 3071532640 50463 SRX23948595 SRS20750284 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30736 30736 SRR28342059 SRX23948594 SRS20750282 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B2 3xflag RESA CLIP input B2 AGN003275   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002508|replicate ref:AGN003275|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 input|replicate label short:RESA CLIP Upf1 #3736 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B2 AGR004055 AGR004055 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004055_R1.fastq AGR004055_R2.fastq fastq fastq 13295917534.0 44026217.0 AGR004055 R1.fastq.zst 0:151 1:151 A:3866188367;C:2751508227;G:3344357660;T:3333805406;N:57874 151 151     3866188367 2751508227 3344357660 3333805406 57874 SRX23948594 SRS20750282 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30737 30737 SRR28342060 SRX23948593 SRS20750285 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B1 3xflag RESA CLIP input B1 AGN003271   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002506|replicate ref:AGN003271|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 input|replicate label short:RESA CLIP Upf1 #3735 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B1 AGR004051 AGR004051 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004051_R1.fastq AGR004051_R2.fastq fastq fastq 14891006336.0 49307968.0 AGR004051 R1.fastq.zst 0:151 1:151 A:4241333172;C:3027167277;G:3764089225;T:3858355544;N:61118 151 151     4241333172 3027167277 3764089225 3858355544 61118 SRX23948593 SRS20750285 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
31884 31884 SRR28747851 SRX24313483 SRS21075233 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 3 Ctrl 3 Ctrl 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-3_S26_L004_R2_001.fastq.gz Ctrl-3_S26_L004_R1_001.fastq.gz fastq fastq 6658139400.0 22193798.0 Ctrl 3 S26 L004 R1 001.fastq.gz 0:150 1:150 A:1953050910;C:1380426193;G:1413459206;T:1911166654;N:36437 150 150     1953050910 1380426193 1413459206 1911166654 36437 SRX24313483 SRS21075233 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94694 0.94695 0.14305 0.14206 0.70412 0.70473 0.59878 0.59922 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31885 31885 SRR28747852 SRX24313482 SRS21075231 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 2 Ctrl 2 Ctrl 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-2_S25_L004_R1_001.fastq.gz Ctrl-2_S25_L004_R2_001.fastq.gz fastq fastq 7515161100.0 25050537.0 Ctrl 2 S25 L004 R1 001.fastq.gz 0:150 1:150 A:2218032458;C:1545198589;G:1580900913;T:2170988635;N:40505 150 150     2218032458 1545198589 1580900913 2170988635 40505 SRX24313482 SRS21075231 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94205 0.94032 0.15138 0.15085 0.69578 0.69645 0.5641 0.56481 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31886 31886 SRR28747853 SRX24313481 SRS21075234 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 1 Ctrl 1 Ctrl 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-1_S24_L004_R1_001.fastq.gz Ctrl-1_S24_L004_R2_001.fastq.gz fastq fastq 9747041100.0 32490137.0 Ctrl 1 S24 L004 R1 001.fastq.gz 0:150 1:150 A:2863031605;C:2014131410;G:2067943208;T:2801881561;N:53316 150 150     2863031605 2014131410 2067943208 2801881561 53316 SRX24313481 SRS21075234 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94378 0.94419 0.14935 0.14934 0.70749 0.7069 0.60161 0.59912 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31887 31887 SRR28747854 SRX24313480 SRS21075232 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 3 4OI 3 4OI 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-3_S23_L004_R1_001.fastq.gz 4OI-3_S23_L004_R2_001.fastq.gz fastq fastq 8273990400.0 27579968.0 4OI 3 S23 L004 R1 001.fastq.gz 0:150 1:150 A:2162937415;C:1975194532;G:2012089890;T:2123723196;N:45367 150 150     2162937415 1975194532 2012089890 2123723196 45367 SRX24313480 SRS21075232 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96535 0.96542 0.03083 0.03097 0.71279 0.71295 0.48276 0.47927 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31888 31888 SRR28747855 SRX24313479 SRS21075230 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 2 4OI 2 4OI 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-2_S28_L003_R1_001.fastq.gz 4OI-2_S28_L003_R2_001.fastq.gz fastq fastq 6579714300.0 21932381.0 4OI 2 S28 L003 R1 001.fastq.gz 0:150 1:150 A:1710345718;C:1580260893;G:1608081826;T:1680921918;N:103945 150 150     1710345718 1580260893 1608081826 1680921918 103945 SRX24313479 SRS21075230 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96511 0.96418 0.03843 0.0384 0.70179 0.7027 0.49174 0.5066 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31889 31889 SRR28747856 SRX24313478 SRS21075229 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 1 4OI 1 4OI 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-1_S27_L003_R1_001.fastq.gz 4OI-1_S27_L003_R2_001.fastq.gz fastq fastq 7099570500.0 23665235.0 4OI 1 S27 L003 R1 001.fastq.gz 0:150 1:150 A:1858012411;C:1693592911;G:1723374425;T:1824476953;N:113800 150 150     1858012411 1693592911 1723374425 1824476953 113800 SRX24313478 SRS21075229 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96619 0.96559 0.04154 0.04152 0.70386 0.70412 0.48321 0.49372 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
32617 32617 SRR29366294 SRX24880743 SRS21589520 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs4   strain:TU|isolate:NPs4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs4 NPs4 A total amount of 9 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0022_good_1.fq.gz Unknown_BO623-04T0022_good_2.fq.gz fastq fastq 6748273836.0 22592809.0 Unknown BO623 04T0022 good 1.fq.gz 0:149.35 1:149.35 A:1774719919;C:1597377190;G:1614927098;T:1761071358;N:178271 149 149     1774719919 1597377190 1614927098 1761071358 178271 SRX24880743 SRS21589520 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32618 32618 SRR29366295 SRX24880742 SRS21589518 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs3   strain:TU|isolate:NPs3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs3 NPs3 A total amount of 8 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0021_good_1.fq.gz Unknown_BO623-04T0021_good_2.fq.gz fastq fastq 6529485490.0 21847936.0 Unknown BO623 04T0021 good 1.fq.gz 0:149.43 1:149.43 A:1717039978;C:1547743896;G:1563982349;T:1700522682;N:196585 149 149     1717039978 1547743896 1563982349 1700522682 196585 SRX24880742 SRS21589518 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32619 32619 SRR29366296 SRX24880741 SRS21589519 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs2   strain:TU|isolate:NPs2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs2 NPs2 A total amount of 7 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0020_good_1.fq.gz Unknown_BO623-04T0020_good_2.fq.gz fastq fastq 6699049910.0 22407080.0 Unknown BO623 04T0020 good 1.fq.gz 0:149.49 1:149.49 A:1761959579;C:1586799482;G:1603631340;T:1746520369;N:139140 149 149     1761959579 1586799482 1603631340 1746520369 139140 SRX24880741 SRS21589519 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32620 32620 SRR29366297 SRX24880740 SRS21589517 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs1   strain:TU|isolate:NPs1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs1 NPs1 A total amount of 6 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0019_good_1.fq.gz Unknown_BO623-04T0019_good_2.fq.gz fastq fastq 6132468788.0 20516184.0 Unknown BO623 04T0019 good 1.fq.gz 0:149.45 1:149.45 A:1607332987;C:1458658424;G:1471957341;T:1594421337;N:98699 149 149     1607332987 1458658424 1471957341 1594421337 98699 SRX24880740 SRS21589517 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32621 32621 SRR29366298 SRX24880739 SRS21589516 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C6   strain:TU|isolate:Control6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C6 C6 A total amount of 5 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0018_good_1.fq.gz Unknown_BO623-04T0018_good_2.fq.gz fastq fastq 5940082248.0 19857041.0 Unknown BO623 04T0018 good 1.fq.gz 0:149.57 1:149.57 A:1533707674;C:1435538751;G:1452812826;T:1517833025;N:189972 149 149     1533707674 1435538751 1452812826 1517833025 189972 SRX24880739 SRS21589516 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32622 32622 SRR29366299 SRX24880738 SRS21589515 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C5   strain:TU|isolate:Control5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C5 C5 A total amount of 4 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0017_good_1.fq.gz Unknown_BO623-04T0017_good_2.fq.gz fastq fastq 6758002932.0 22599590.0 Unknown BO623 04T0017 good 1.fq.gz 0:149.52 1:149.52 A:1739766340;C:1637642157;G:1652002401;T:1728330255;N:261779 149 149     1739766340 1637642157 1652002401 1728330255 261779 SRX24880738 SRS21589515 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32623 32623 SRR29366300 SRX24880737 SRS21589514 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C4   strain:TU|isolate:Control4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C4 C4 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0016_good_1.fq.gz Unknown_BO623-04T0016_good_2.fq.gz fastq fastq 6210972784.0 20767744.0 Unknown BO623 04T0016 good 1.fq.gz 0:149.53 1:149.53 A:1591917700;C:1506245368;G:1529628371;T:1583090947;N:90398 149 149     1591917700 1506245368 1529628371 1583090947 90398 SRX24880737 SRS21589514 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32624 32624 SRR29366301 SRX24880736 SRS21589513 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C3   strain:TU|isolate:Control3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C3 C3 A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0015_good_1.fq.gz Unknown_BO623-04T0015_good_2.fq.gz fastq fastq 6666249022.0 22284306.0 Unknown BO623 04T0015 good 1.fq.gz 0:149.57 1:149.57 A:1722337869;C:1610144787;G:1630507947;T:1703082771;N:175648 149 149     1722337869 1610144787 1630507947 1703082771 175648 SRX24880736 SRS21589513 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32625 32625 SRR29366302 SRX24880735 SRS21589512 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs6   strain:TU|isolate:NPs6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs6 NPs6 A total amount of11 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0024_good_1.fq.gz Unknown_BO623-04T0024_good_2.fq.gz fastq fastq 6819262402.0 22797722.0 Unknown BO623 04T0024 good 1.fq.gz 0:149.56 1:149.56 A:1781861689;C:1629655448;G:1645382478;T:1762184452;N:178335 149 149     1781861689 1629655448 1645382478 1762184452 178335 SRX24880735 SRS21589512 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32626 32626 SRR29366303 SRX24880734 SRS21589511 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs5   strain:TU|isolate:NPs5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs5 NPs5 A total amount of10 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0023_good_1.fq.gz Unknown_BO623-04T0023_good_2.fq.gz fastq fastq 6773730348.0 22673915.0 Unknown BO623 04T0023 good 1.fq.gz 0:149.37 1:149.37 A:1779182337;C:1607164031;G:1624141377;T:1763062617;N:179986 149 149     1779182337 1607164031 1624141377 1763062617 179986 SRX24880734 SRS21589511 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32627 32627 SRR29366304 SRX24880733 SRS21589509 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C2   strain:TU|isolate:Control2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C2 C2 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following manufacturers recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37C for 15 min followed by 5 min at 95C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0014_good_1.fq.gz Unknown_BO623-04T0014_good_2.fq.gz fastq fastq 6805354296.0 22755187.0 Unknown BO623 04T0014 good 1.fq.gz 0:149.53 1:149.53 A:1742825793;C:1651738009;G:1677448209;T:1733168084;N:174201 149 149     1742825793 1651738009 1677448209 1733168084 174201 SRX24880733 SRS21589509 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32628 32628 SRR29366305 SRX24880732 SRS21589510 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C1   strain:TU|isolate:Control1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C1 C1 A total amount of 0 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0013_good_1.fq.gz Unknown_BO623-04T0013_good_2.fq.gz fastq fastq 6546144006.0 21896126.0 Unknown BO623 04T0013 good 1.fq.gz 0:149.48 1:149.48 A:1688579059;C:1582023304;G:1598552166;T:1676633897;N:355580 149 149     1688579059 1582023304 1598552166 1676633897 355580 SRX24880732 SRS21589510 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
33369 33369 SRR30159204 SRX25626516 SRS22271512 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Mutant 2   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.8 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Mutant 2 Li lab 003 4 Li lab 003 4 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 6 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     7c166f592635e7a5f904d56dd661e1cc mut-2_1.fq.gz.gz 3adc1733ac4cb77beca49461cb17544b mut-2_2.fq.gz.gz fastq fastq 5518961400.0 18396538.0 3adc1733ac4cb77beca49461cb17544b mut 2 2.fq.gz.gz 0:150 1:150 A:1469924277;C:1285547670;G:1307420673;T:1455990444;N:78336 150 150     1469924277 1285547670 1307420673 1455990444 78336 SRX25626516 SRS22271512 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96085 0.95919 0.05548 0.05519 0.7207 0.72178 0.47759 0.47549 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33370 33370 SRR30159205 SRX25626515 SRS22271511 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Mutant 1   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.7 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Mutant 1 Li lab 003 3 Li lab 003 3 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 5 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     39cb7947119cec5afac3df66c0ae0048 mut-1_1.fq.gz.gz 1bfc59902758bb1cbf8eb4549d3375fd mut-1_2.fq.gz.gz fastq fastq 5947120500.0 19823735.0 1bfc59902758bb1cbf8eb4549d3375fd mut 1 2.fq.gz.gz 0:150 1:150 A:1567673549;C:1401761128;G:1423907629;T:1553701047;N:77147 150 150     1567673549 1401761128 1423907629 1553701047 77147 SRX25626515 SRS22271511 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96303 0.96203 0.05003 0.04984 0.72271 0.72299 0.47608 0.47831 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33371 33371 SRR30159206 SRX25626514 SRS22271510 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Wild type 2   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.6 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Wild type 2 Li lab 003 2 Li lab 003 2 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 4 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     4376e7007befe0cf23ffa7f9dd62512c sib-3_1.fq.gz.gz da4d46fd26ca22e90409489640659b1c sib-3_2.fq.gz.gz fastq fastq 6113935200.0 20379784.0 4376e7007befe0cf23ffa7f9dd62512c sib 3 1.fq.gz.gz 0:150 1:150 A:1609711214;C:1443384557;G:1461871812;T:1598876167;N:91450 150 150     1609711214 1443384557 1461871812 1598876167 91450 SRX25626514 SRS22271510 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.95947 0.9591 0.04902 0.0492 0.71707 0.71796 0.46871 0.4604 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33372 33372 SRR30159207 SRX25626513 SRS22271509 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Wild type 1   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.5 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Wild type 1 Li lab 003 1 Li lab 003 1 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 3 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     319b2e8b61305a8937eb903a7a20a2e7 sib-2_1.fq.gz.gz 4a84982431b5360126f279ceabf00548 sib-2_2.fq.gz.gz fastq fastq 6351813000.0 21172710.0 319b2e8b61305a8937eb903a7a20a2e7 sib 2 1.fq.gz.gz 0:150 1:150 A:1674596701;C:1497102731;G:1525030471;T:1654985592;N:97505 150 150     1674596701 1497102731 1525030471 1654985592 97505 SRX25626513 SRS22271509 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96469 0.96334 0.04679 0.04633 0.73119 0.73198 0.47359 0.47265 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33373 33373 SRR30168925 SRX25635545 SRS22279934 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax Ti 3d3 Z Hi 3d3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:inhibition 3|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z Hi 3d3 Z Hi 3d3 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_Hi_3d3_R2.fastq Z_Hi_3d3_R1.fastq fastq fastq 6296371726.0 20848913.0 Z Hi 3d3 R1.fastq 0:151 1:151 A:1704155951;C:1439352121;G:1462544186;T:1690244568;N:74900 151 151     1704155951 1439352121 1462544186 1690244568 74900 SRX25635545 SRS22279934 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.9328 0.93327 0.07548 0.07488 0.71985 0.71928 0.5049 0.50889 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33374 33374 SRR30168926 SRX25635544 SRS22279933 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax Ti 3d2 Z Hi 3d2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:inhibition 2|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z Hi 3d2 Z Hi 3d2 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_Hi_3d2_R1.fastq Z_Hi_3d2_R2.fastq fastq fastq 6530683862.0 21624781.0 Z Hi 3d2 R1.fastq 0:151 1:151 A:1754695891;C:1502355303;G:1526937743;T:1746614271;N:80654 151 151     1754695891 1502355303 1526937743 1746614271 80654 SRX25635544 SRS22279933 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.93139 0.93214 0.08116 0.08178 0.70981 0.70983 0.48395 0.48661 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33375 33375 SRR30168927 SRX25635543 SRS22279932 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax Ti 3d1 Z Hi 3d1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:inhibition 1|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z Hi 3d1 Z Hi 3d1 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_Hi_3d1_R1.fastq Z_Hi_3d1_R2.fastq fastq fastq 6160626350.0 20399425.0 Z Hi 3d1 R1.fastq 0:151 1:151 A:1667594818;C:1407434381;G:1429290724;T:1656232741;N:73686 151 151     1667594818 1407434381 1429290724 1656232741 73686 SRX25635543 SRS22279932 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.9337 0.93249 0.08009 0.08009 0.71242 0.71338 0.47654 0.47528 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33376 33376 SRR30168928 SRX25635542 SRS22279930 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax C 3d3 Z c 3d3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:n1 3|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z c 3d3 Z c 3d3 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_C_3d3_R2.fastq Z_C_3d3_R1.fastq fastq fastq 5810255010.0 19239255.0 Z C 3d3 R1.fastq 0:151 1:151 A:1564226440;C:1336263606;G:1355696622;T:1553998418;N:69924 151 151     1564226440 1336263606 1355696622 1553998418 69924 SRX25635542 SRS22279930 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.92958 0.92832 0.07821 0.07745 0.70463 0.70569 0.47036 0.47581 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33377 33377 SRR30168929 SRX25635541 SRS22279931 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax C 3d2 Z c 3d2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:n1 2|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z c 3d2 Z c 3d2 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_C_3d2_R2.fastq Z_C_3d2_R1.fastq fastq fastq 6856714606.0 22704353.0 Z C 3d2 R1.fastq 0:151 1:151 A:1850156301;C:1573942247;G:1595025700;T:1837509085;N:81273 151 151     1850156301 1573942247 1595025700 1837509085 81273 SRX25635541 SRS22279931 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.92587 0.92539 0.08056 0.08087 0.70343 0.70423 0.48091 0.47768 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33378 33378 SRR30168930 SRX25635540 SRS22279929 SRP524879 PRJNA1145574 RNA sequencing of tail fin of zebrafish PRJNA1145574 Other gene expression change post inhibition of HSP90       Ax C 3d1 Z c 3d1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3.5 month|collection date:2022 11 20|geo loc name:missing|sex:not determined|tissue:tail fin|treatment:n1 1|BioSampleModel:Model organism or animal                 tail fin regeneration of zebrafish Z c 3d1 Z c 3d1 cDNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP524879     Z_C_3d1_R1.fastq Z_C_3d1_R2.fastq fastq fastq 5915874074.0 19588987.0 Z C 3d1 R1.fastq 0:151 1:151 A:1601403264;C:1350219159;G:1374928971;T:1589252208;N:70472 151 151     1601403264 1350219159 1374928971 1589252208 70472 SRX25635540 SRS22279929 SRA1942523 Ocean University of China|Department of marine biology Ocean University of China 2 0.92552 0.92878 0.07906 0.07985 0.70264 0.70323 0.48016 0.48019 151 151 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-08 Adult Adult Multi-tissue Multi-system
33916 33916 SRR30920839 SRX26323786 SRS22850830 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iv 1   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 PF iv 1 PF iv 1 PF iv 1 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iv_1_1.fq.gz PF_iv_1_2.fq.gz fastq fastq 7070670900.0 23568903.0 PF iv 1 1.fq.gz 0:150 1:150 A:1943964885;C:1626486936;G:1603332965;T:1896802175;N:83939 150 150     1943964885 1626486936 1603332965 1896802175 83939 SRX26323786 SRS22850830 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33917 33917 SRR30920840 SRX26323785 SRS22850828 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iii 3   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 PF iii 3 PF iii 3 PF iii 3 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iii_3_1.fq.gz PF_iii_3_2.fq.gz fastq fastq 6934323600.0 23114412.0 PF iii 3 1.fq.gz 0:150 1:150 A:1813397404;C:1659011482;G:1680744429;T:1781143700;N:26585 150 150     1813397404 1659011482 1680744429 1781143700 26585 SRX26323785 SRS22850828 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33918 33918 SRR30920841 SRX26323784 SRS22850835 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iii 2   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 PF iii 2 PF iii 2 PF iii 2 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iii_2_1.fq.gz PF_iii_2_2.fq.gz fastq fastq 7255113000.0 24183710.0 PF iii 2 1.fq.gz 0:150 1:150 A:1877711956;C:1751268862;G:1779105498;T:1846998314;N:28370 150 150     1877711956 1751268862 1779105498 1846998314 28370 SRX26323784 SRS22850835 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33919 33919 SRR30920842 SRX26323783 SRS22850829 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iii 1   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 PF iii 1 PF iii 1 PF iii 1 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iii_1_1.fq.gz PF_iii_1_2.fq.gz fastq fastq 7367112000.0 24557040.0 PF iii 1 1.fq.gz 0:150 1:150 A:1943591568;C:1745588879;G:1774109048;T:1903793252;N:29253 150 150     1943591568 1745588879 1774109048 1903793252 29253 SRX26323783 SRS22850829 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33920 33920 SRR30920843 SRX26323782 SRS22850827 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF ii 3   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 PF ii 3 PF ii 3 PF ii 3 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_ii_3_1.fq.gz PF_ii_3_2.fq.gz fastq fastq 7076391300.0 23587971.0 PF ii 3 1.fq.gz 0:150 1:150 A:1894076667;C:1654017021;G:1661713202;T:1866530077;N:54333 150 150     1894076667 1654017021 1661713202 1866530077 54333 SRX26323782 SRS22850827 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33921 33921 SRR30920844 SRX26323781 SRS22850824 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF ii 2   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 PF ii 2 PF ii 2 PF ii 2 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_ii_2_1.fq.gz PF_ii_2_2.fq.gz fastq fastq 7019128200.0 23397094.0 PF ii 2 1.fq.gz 0:150 1:150 A:1864708472;C:1652262592;G:1662746794;T:1839356863;N:53479 150 150     1864708472 1652262592 1662746794 1839356863 53479 SRX26323781 SRS22850824 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33922 33922 SRR30920845 SRX26323780 SRS22850826 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF ii 1   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China:Changsha|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 PF ii 1 PF ii 1 PF ii 1 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_ii_1_1.fq.gz PF_ii_1_2.fq.gz fastq fastq 8013867900.0 26712893.0 PF ii 1 1.fq.gz 0:150 1:150 A:2115645121;C:1898389790;G:1909480370;T:2090291064;N:61555 150 150     2115645121 1898389790 1909480370 2090291064 61555 SRX26323780 SRS22850826 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33923 33923 SRR30920846 SRX26323779 SRS22850825 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF i 3   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 PF i 3 PF i 3 PF i 3 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_i_3_1.fq.gz PF_i_3_2.fq.gz fastq fastq 8319390000.0 27731300.0 PF i 3 1.fq.gz 0:150 1:150 A:2161188519;C:1997121516;G:2035390212;T:2125657588;N:32165 150 150     2161188519 1997121516 2035390212 2125657588 32165 SRX26323779 SRS22850825 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33924 33924 SRR30920847 SRX26323778 SRS22850823 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iv 3   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 PF iv 3 PF iv 3 PF iv 3 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iv_3_1.fq.gz PF_iv_3_2.fq.gz fastq fastq 7173257700.0 23910859.0 PF iv 3 1.fq.gz 0:150 1:150 A:1875724697;C:1713434205;G:1745363776;T:1838706880;N:28142 150 150     1875724697 1713434205 1745363776 1838706880 28142 SRX26323778 SRS22850823 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33925 33925 SRR30920848 SRX26323777 SRS22850821 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF iv 2   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 PF iv 2 PF iv 2 PF iv 2 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_iv_2_1.fq.gz PF_iv_2_2.fq.gz fastq fastq 7161631500.0 23872105.0 PF iv 2 1.fq.gz 0:150 1:150 A:1890379638;C:1697508923;G:1718050265;T:1855664701;N:27973 150 150     1890379638 1697508923 1718050265 1855664701 27973 SRX26323777 SRS22850821 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33926 33926 SRR30920849 SRX26323776 SRS22850822 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF i 2   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 PF i 2 PF i 2 PF i 2 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_i_2_1.fq.gz PF_i_2_2.fq.gz fastq fastq 7036742700.0 23455809.0 PF i 2 1.fq.gz 0:150 1:150 A:1861224200;C:1662236616;G:1671149144;T:1842079812;N:52928 150 150     1861224200 1662236616 1671149144 1842079812 52928 SRX26323776 SRS22850822 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
33927 33927 SRR30920850 SRX26323775 SRS22850820 SRP537366 PRJNA1169999 Danio rerio Raw sequence reads PRJNA1169999 Other Transcriptional analysis of zebrafish         PF i 1   strain:not collecte|age:3 mpf|collection date:2023 06|geo loc name:China|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 PF i 1 PF i 1 PF i 1 the primary follicles of zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP537366     PF_i_1_1.fq.gz PF_i_1_2.fq.gz fastq fastq 6977957400.0 23259858.0 PF i 1 1.fq.gz 0:150 1:150 A:1821299728;C:1674791787;G:1691820873;T:1790017865;N:27147 150 150     1821299728 1674791787 1691820873 1790017865 27147 SRX26323775 SRS22850820 SRA1988616 Hunan Normal University|School of Life Sciences Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-09 Adult Adult Gonad Reproductive System
34100 34100 SRR31179089 SRX26561802 SRS23067260 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         L21 L1EIC0700904 T L2.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:9|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain L21 L21 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700904-T_L2.R1.raw.fastq.gz L1EIC0700904-T_L2.R2.raw.fastq.gz fastq fastq 6755197306.0 22368203.0 L1EIC0700904 T L2.R1.raw.fastq.gz 0:151 1:151 A:1778527472;C:1586407415;G:1611223994;T:1770639781;N:8398644 151 151     1778527472 1586407415 1611223994 1770639781 8398644 SRX26561802 SRS23067260 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34101 34101 SRR31179090 SRX26561801 SRS23067261 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         L11 L1EIC0700903 T L1.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:7|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain L11 L11 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700903-T_L1.R1.raw.fastq.gz L1EIC0700903-T_L1.R2.raw.fastq.gz fastq fastq 7262619518.0 24048409.0 L1EIC0700903 T L1.R1.raw.fastq.gz 0:151 1:151 A:1897564712;C:1719515913;G:1744510723;T:1891980402;N:9047768 151 151     1897564712 1719515913 1744510723 1891980402 9047768 SRX26561801 SRS23067261 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34102 34102 SRR31179091 SRX26561800 SRS23067257 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         C31 L1EIC0700902 T C3.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:5|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain C31 C31 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700902-T_C3.R1.raw.fastq.gz L1EIC0700902-T_C3.R2.raw.fastq.gz fastq fastq 6986250560.0 23133280.0 L1EIC0700902 T C3.R1.raw.fastq.gz 0:151 1:151 A:1814714141;C:1667167814;G:1686637674;T:1809014055;N:8716876 151 151     1814714141 1667167814 1686637674 1809014055 8716876 SRX26561800 SRS23067257 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34103 34103 SRR31179092 SRX26561799 SRS23067259 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         C21 L1EIC0700901 T C2.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain C21 C21 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700901-T_C2.R1.raw.fastq.gz L1EIC0700901-T_C2.R2.raw.fastq.gz fastq fastq 7084353146.0 23458123.0 L1EIC0700901 T C2.R1.raw.fastq.gz 0:151 1:151 A:1860686893;C:1670094870;G:1691858523;T:1852823738;N:8889122 151 151     1860686893 1670094870 1691858523 1852823738 8889122 SRX26561799 SRS23067259 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34104 34104 SRR31179093 SRX26561798 SRS23067255 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         S31 L1EIC0700908 T S3.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:17|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain S31 S31 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700908-T_S3.R1.raw.fastq.gz L1EIC0700908-T_S3.R2.raw.fastq.gz fastq fastq 6992611888.0 23154344.0 L1EIC0700908 T S3.R1.raw.fastq.gz 0:151 1:151 A:1891265867;C:1594515809;G:1615494569;T:1882648469;N:8687174 151 151     1891265867 1594515809 1615494569 1882648469 8687174 SRX26561798 SRS23067255 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34105 34105 SRR31179094 SRX26561797 SRS23067258 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         S21 L1EIC0700907 T S2.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:15|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain S21 S21 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700907-T_S2.R1.raw.fastq.gz L1EIC0700907-T_S2.R2.raw.fastq.gz fastq fastq 6223201958.0 20606629.0 L1EIC0700907 T S2.R1.raw.fastq.gz 0:151 1:151 A:1635455481;C:1467707544;G:1484789988;T:1627505187;N:7743758 151 151     1635455481 1467707544 1484789988 1627505187 7743758 SRX26561797 SRS23067258 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34106 34106 SRR31179095 SRX26561796 SRS23067256 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         S11 L1EIC0700906 T S1.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:13|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain S11 S11 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700906-T_S1.R1.raw.fastq.gz L1EIC0700906-T_S1.R2.raw.fastq.gz fastq fastq 6882679660.0 22790330.0 L1EIC0700906 T S1.R1.raw.fastq.gz 0:151 1:151 A:1805328115;C:1625761692;G:1646060059;T:1796837143;N:8692651 151 151     1805328115 1625761692 1646060059 1796837143 8692651 SRX26561796 SRS23067256 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34107 34107 SRR31179096 SRX26561795 SRS23067254 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         L31 L1EIC0700905 T L3.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:11|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain L31 L31 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700905-T_L3.R1.raw.fastq.gz L1EIC0700905-T_L3.R2.raw.fastq.gz fastq fastq 6901039146.0 22851123.0 L1EIC0700905 T L3.R1.raw.fastq.gz 0:151 1:151 A:1796093025;C:1641065561;G:1664159837;T:1791078184;N:8642539 151 151     1796093025 1641065561 1664159837 1791078184 8642539 SRX26561795 SRS23067254 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34108 34108 SRR31179097 SRX26561794 SRS23067253 SRP542312 PRJNA1180208 RNA Sequencing of NPs in zebrafish brain PRJNA1180208 Other         C11 L1EIC0700900 T C1.R1   strain:AB|age:Adult|collection date:not applicable|geo loc name:Hong Kong|sex:not applicable|tissue:Brain|Tmp:1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish brain C11 C11 Adult zebrafish brain     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 3000   SRP542312     L1EIC0700900-T_C1.R1.raw.fastq.gz L1EIC0700900-T_C1.R2.raw.fastq.gz fastq fastq 10565913034.0 34986467.0 L1EIC0700900 T C1.R1.raw.fastq.gz 0:151 1:151 A:2737543425;C:2523674862;G:2563177427;T:2728317948;N:13199372 151 151     2737543425 2523674862 2563177427 2728317948 13199372 SRX26561794 SRS23067253 SRA2001903 City University of Hong Kong|School of Energy and Environmental City University of Hong Kong                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-10-31 Adult Adult Brain Nervous System
34128 34128 SRR31371655 SRX26745254 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PC3 R1.fq PC3 R1.fq CuNPs and melatonin treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PC3_R1.fq.gz PC3_R2.fq.gz fastq fastq 8050557450.0 26657475.0 PC3 R1.fq.gz                       SRX26745254 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34129 34129 SRR31371656 SRX26745253 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PC2 R1.fq PC2 R1.fq CuNPs and melatonin treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PC2_R1.fq.gz PC2_R2.fq.gz fastq fastq 7072903722.0 23420211.0 PC2 R1.fq.gz 0:151 1:151 A:1848366962;C:1685927772;G:1702568524;T:1835518466;N:521998 151 151     1848366962 1685927772 1702568524 1835518466 521998 SRX26745253 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34130 34130 SRR31371657 SRX26745252 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PC1 R1.fq PC1 R1.fq CuNPs and melatonin treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PC1_R1.fq.gz PC1_R2.fq.gz fastq fastq 9551575668.0 31627734.0 PC1 R1.fq.gz                       SRX26745252 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34131 34131 SRR31371658 SRX26745251 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PB3 R1.fq PB3 R1.fq CuNPs treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PB3_R1.fq.gz PB3_R2.fq.gz fastq fastq 6839092000.0 22646000.0 PB3 R1.fq.gz                       SRX26745251 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34132 34132 SRR31371659 SRX26745250 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PB2 R1.fq PB2 R1.fq CuNPs treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PB2_R1.fq.gz PB2_R2.fq.gz fastq fastq 7582292558.0 25106929.0 PB2 R1.fq.gz                       SRX26745250 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34133 34133 SRR31371660 SRX26745249 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish PB1 R1.fq PB1 R1.fq CuNPs treatment     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     PB1_R1.fq.gz PB1_R2.fq.gz fastq fastq 8122972218.0 26897259.0 PB1 R1.fq.gz                       SRX26745249 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34134 34134 SRR31371661 SRX26745248 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish CA3 R1.fq CA3 R1.fq control     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     CA3_R1.fq.gz CA3_R2.fq.gz fastq fastq 7638136586.0 25291843.0 CA3 R1.fq.gz                       SRX26745248 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34135 34135 SRR31371662 SRX26745247 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish CA1 R1.fq CA1 R1.fq control     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     CA1_R1.fq.gz CA1_R2.fq.gz fastq fastq 7499744784.0 24833592.0 CA1 R1.fq.gz 0:151 1:151 A:1951636355;C:1801626786;G:1812560367;T:1933366696;N:554580 151 151     1951636355 1801626786 1812560367 1933366696 554580 SRX26745247 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34136 34136 SRR31371663 SRX26745246 SRS23234144 SRP545712 PRJNA1186363 Danio rerio Transcriptome or Gene expression PRJNA1186363 Other Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin       Model organism or animal sample from zebrafish zebra001   cultivar:zebrafish|age:40dpf|collection date:2024 11 15|geo loc name:China|sex:female|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences|zebrafish:Gonadal development|BioSampleModel:Model organism or animal                 RNA seq from the gonad of Zebrafish CA2 R1.fq CA2 R1.fq control     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP545712     CA2_R1.fq.gz CA2_R2.fq.gz fastq fastq 6253035330.0 20705415.0 CA2 R1.fq.gz                       SRX26745246 SRS23234144 SRA2016483 Chinese Academy of Fishery Science|Freshwater Fishery Research Center Chinese Academy of Fishery Science                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-11-17 Juvenile Juvenile Gonad Reproductive System
34409 34409 SRR31747815 SRX27109876 SRS23567839 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         AFB2   strain:not collected|isolate:liver AFB2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172628 LRA172628 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     AFB2_R1.fastq.gz AFB2_R2.fastq.gz fastq fastq 7190069454.0 23808177.0 AFB2 R1.fastq.gz 0:151 1:151 A:2078244342;C:1510893083;G:1547178609;T:2053626767;N:126653 151 151     2078244342 1510893083 1547178609 2053626767 126653 SRX27109876 SRS23567839 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34410 34410 SRR31747816 SRX27109875 SRS23567837 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         AFB1   strain:not collected|isolate:liver AFB1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172627 LRA172627 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     AFB1_R1.fastq.gz AFB1_R2.fastq.gz fastq fastq 7463779000.0 24714500.0 AFB1 R1.fastq.gz 0:151 1:151 A:2176506326;C:1554667596;G:1582400568;T:2150036004;N:168506 151 151     2176506326 1554667596 1582400568 2150036004 168506 SRX27109875 SRS23567837 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34411 34411 SRR31747817 SRX27109874 SRS23567838 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         EPO4   strain:not collected|isolate:liver EPO4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172635 LRA172635 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     EPO4_R1.fastq.gz EPO4_R2.fastq.gz fastq fastq 8273309328.0 27395064.0 EPO4 R1.fastq.gz 0:151 1:151 A:2390853071;C:1742121394;G:1771230346;T:2368915323;N:189194 151 151     2390853071 1742121394 1771230346 2368915323 189194 SRX27109874 SRS23567838 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34412 34412 SRR31747818 SRX27109873 SRS23567836 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         EPO3   strain:not collected|isolate:liver EPO3|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172634 LRA172634 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     EPO3_R1.fastq.gz EPO3_R2.fastq.gz fastq fastq 7097420082.0 23501391.0 EPO3 R1.fastq.gz 0:151 1:151 A:2092952383;C:1451623472;G:1477150205;T:2075535584;N:158438 151 151     2092952383 1451623472 1477150205 2075535584 158438 SRX27109873 SRS23567836 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34413 34413 SRR31747819 SRX27109872 SRS23567834 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         EPO2   strain:not collected|isolate:liver EPO2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172633 LRA172633 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     EPO2_R1.fastq.gz EPO2_R2.fastq.gz fastq fastq 7332924514.0 24281207.0 EPO2 R1.fastq.gz 0:151 1:151 A:2162671338;C:1496551996;G:1515648771;T:2157891639;N:160770 151 151     2162671338 1496551996 1515648771 2157891639 160770 SRX27109872 SRS23567834 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34414 34414 SRR31747820 SRX27109871 SRS23567835 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         EPO1   strain:not collected|isolate:liver EPO1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172632 LRA172632 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     EPO1_R1.fastq.gz EPO1_R2.fastq.gz fastq fastq 8287626544.0 27442472.0 EPO1 R1.fastq.gz 0:151 1:151 A:2435156330;C:1694808350;G:1717315788;T:2440143946;N:202130 151 151     2435156330 1694808350 1717315788 2440143946 202130 SRX27109871 SRS23567835 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34415 34415 SRR31747821 SRX27109870 SRS23567833 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         CK5   strain:not collected|isolate:liver CK4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172626 LRA172626 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     CK5_R1.fastq.gz CK5_R2.fastq.gz fastq fastq 7157140280.0 23699140.0 CK5 R1.fastq.gz 0:151 1:151 A:2092635667;C:1492801085;G:1512780390;T:2058759456;N:163682 151 151     2092635667 1492801085 1512780390 2058759456 163682 SRX27109870 SRS23567833 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34416 34416 SRR31747822 SRX27109869 SRS23567832 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         CK4   strain:not collected|isolate:liver CK3|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172625 LRA172625 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     CK4_R1.fastq.gz CK4_R2.fastq.gz fastq fastq 5903236582.0 19547141.0 CK4 R1.fastq.gz 0:151 1:151 A:1649245280;C:1297061493;G:1327173777;T:1629624071;N:131961 151 151     1649245280 1297061493 1327173777 1629624071 131961 SRX27109869 SRS23567832 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34417 34417 SRR31747823 SRX27109868 SRS23567831 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         COM5   strain:not collected|isolate:liver COM4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172641 LRA172641 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     COM5_R1.fastq.gz COM5_R2.fastq.gz fastq fastq 7598066924.0 25159162.0 COM5 R1.fastq.gz 0:151 1:151 A:2223131767;C:1578956803;G:1603115446;T:2192694602;N:168306 151 151     2223131767 1578956803 1603115446 2192694602 168306 SRX27109868 SRS23567831 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34418 34418 SRR31747824 SRX27109867 SRS23567830 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         COM4   strain:not collected|isolate:liver COM3|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172640 LRA172640 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     COM4_R1.fastq.gz COM4_R2.fastq.gz fastq fastq 7633749130.0 25277315.0 COM4 R1.fastq.gz 0:151 1:151 A:2223410712;C:1603699864;G:1630586500;T:2175879626;N:172428 151 151     2223410712 1603699864 1630586500 2175879626 172428 SRX27109867 SRS23567830 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34419 34419 SRR31747825 SRX27109866 SRS23567829 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         COM3   strain:not collected|isolate:liver COM2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172639 LRA172639 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     COM3_R1.fastq.gz COM3_R2.fastq.gz fastq fastq 7474959946.0 24751523.0 COM3 R1.fastq.gz 0:151 1:151 A:2145268206;C:1597121014;G:1632808908;T:2099584265;N:177553 151 151     2145268206 1597121014 1632808908 2099584265 177553 SRX27109866 SRS23567829 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34420 34420 SRR31747826 SRX27109865 SRS23567827 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         COM2   strain:not collected|isolate:liver COM1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172638 LRA172638 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     COM2_R1.fastq.gz COM2_R2.fastq.gz fastq fastq 8791460090.0 29110795.0 COM2 R1.fastq.gz 0:151 1:151 A:2541630685;C:1869577126;G:1894336180;T:2485706665;N:209434 151 151     2541630685 1869577126 1894336180 2485706665 209434 SRX27109865 SRS23567827 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34421 34421 SRR31747827 SRX27109864 SRS23567828 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         AFB4   strain:not collected|isolate:liver AFB4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172630 LRA172630 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     AFB4_R1.fastq.gz AFB4_R2.fastq.gz fastq fastq 7267902102.0 24065901.0 AFB4 R1.fastq.gz 0:151 1:151 A:2123758982;C:1506909715;G:1535054542;T:2102016033;N:162830 151 151     2123758982 1506909715 1535054542 2102016033 162830 SRX27109864 SRS23567828 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34422 34422 SRR31747828 SRX27109863 SRS23567826 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         AFB3   strain:not collected|isolate:liver AFB3|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172629 LRA172629 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     AFB3_R1.fastq.gz AFB3_R2.fastq.gz fastq fastq 6300108070.0 20861285.0 AFB3 R1.fastq.gz 0:151 1:151 A:1796927680;C:1350016175;G:1379242261;T:1773425050;N:496904 151 151     1796927680 1350016175 1379242261 1773425050 496904 SRX27109863 SRS23567826 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34423 34423 SRR31747829 SRX27109862 SRS23567825 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         CK2   strain:not collected|isolate:liver CK2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172623 LRA172623 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     CK2_R1.fastq.gz CK2_R2.fastq.gz fastq fastq 6706705770.0 22207635.0 CK2 R1.fastq.gz 0:151 1:151 A:1918005955;C:1429871875;G:1469836872;T:1888840563;N:150505 151 151     1918005955 1429871875 1469836872 1888840563 150505 SRX27109862 SRS23567825 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34424 34424 SRR31747830 SRX27109861 SRS23567824 SRP552011 PRJNA1199330 Transcriptomic analysis of zebrafish liver PRJNA1199330 Other The liver of adult female zebrafish was analyzed.Subsequently RNA seq results were used to explore the key mechanisms of liver damage caused by single and combined exposure to EPO and AFB1.         CK1   strain:not collected|isolate:liver CK1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:liver|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172622 LRA172622 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552011     CK1_R1.fastq.gz CK1_R2.fastq.gz fastq fastq 6319435768.0 20925284.0 CK1 R1.fastq.gz 0:151 1:151 A:1793805737;C:1361852588;G:1396171190;T:1767105304;N:500949 151 151     1793805737 1361852588 1396171190 1767105304 500949 SRX27109861 SRS23567824 SRA2036115 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Liver Liver and Biliary System
34425 34425 SRR31754963 SRX27116846 SRS23574567 SRP552202 PRJNA1199694 Zebrafish ovarian RNA seq PRJNA1199694 Other Adult female zebrafish ovaries were taken for subsequent analyses.In this study we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.         ovary AFB2   strain:not collected|isolate:ovary AFB2|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172648 LRA172648 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552202     AFB2_R2.fastq.gz AFB2_R1.fastq.gz fastq fastq 8264268656.0 27365128.0 AFB2 R1.fastq.gz 0:151 1:151 A:2181967333;C:1933268479;G:1966876338;T:2182007880;N:148626 151 151     2181967333 1933268479 1966876338 2182007880 148626 SRX27116846 SRS23574567 SRA2036776 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Gonad Reproductive System
34426 34426 SRR31754964 SRX27116845 SRS23574566 SRP552202 PRJNA1199694 Zebrafish ovarian RNA seq PRJNA1199694 Other Adult female zebrafish ovaries were taken for subsequent analyses.In this study we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.         ovary AFB1   strain:not collected|isolate:ovary AFB1|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172647 LRA172647 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552202     AFB1_R1.fastq.gz AFB1_R2.fastq.gz fastq fastq 8208094240.0 27179120.0 AFB1 R1.fastq.gz 0:151 1:151 A:2198424448;C:1899278946;G:1926174417;T:2184068899;N:147530 151 151     2198424448 1899278946 1926174417 2184068899 147530 SRX27116845 SRS23574566 SRA2036776 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Gonad Reproductive System
34427 34427 SRR31754965 SRX27116844 SRS23574565 SRP552202 PRJNA1199694 Zebrafish ovarian RNA seq PRJNA1199694 Other Adult female zebrafish ovaries were taken for subsequent analyses.In this study we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.         ovary EPO4   strain:not collected|isolate:ovary EPO4|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172655 LRA172655 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552202     EPO4_R1.fastq.gz EPO4_R2.fastq.gz fastq fastq 6421073868.0 21261834.0 EPO4 R1.fastq.gz 0:151 1:151 A:1714628675;C:1485463411;G:1507815048;T:1712492241;N:674493 151 151     1714628675 1485463411 1507815048 1712492241 674493 SRX27116844 SRS23574565 SRA2036776 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-17 Adult Adult Gonad Reproductive System
34428 34428 SRR31754966 SRX27116843 SRS23574564 SRP552202 PRJNA1199694 Zebrafish ovarian RNA seq PRJNA1199694 Other Adult female zebrafish ovaries were taken for subsequent analyses.In this study we used RNA seq results to uncover the key pathways involved in ovarian damage caused by single and combined exposure to EPO and AFB1.         ovary EPO3   strain:not collected|isolate:ovary EPO3|breed:bred in tanks|cultivar:not collected|ecotype:wild type AB|age:7 mpf|dev stage:Adult zebrafish|collection date:2023 12 03|geo loc name:China: Zhejiang|sex:female|tissue:ovary|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 transcriptomic sequencing LRA172654 LRA172654 The mRNA with polyA tail was enriched by OligodT magnetic beads to construct a library     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP552202     EPO3_R1.fastq.gz EPO3_R2.fastq.gz fastq fastq 12384393350.0 41007925.0 EPO3 R1.fastq.gz 0:151 1:151 A:3299390090;C:2870219776;G:2921073783;T:3292432295;N:1277406 151 151     3299390090 2870219776 2921073783 3292432295 1277406 SRX27116843 SRS23574564 SRA2036776 shandong university|School of Public Health shandong university                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2024-12-18 Adult Adult Gonad Reproductive 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");;