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
30599,SRR27865238,SRX23527802,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con MO,6,6,con MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,con-KDM_1.fq.gz con-KDM_2.fq.gz,fastq fastq,7088132100.0,23627107.0,con KDM 1.fq.gz,0:150 1:150,A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033,150,150,,,1893419600,1649526065,1662549202,1882459200,178033,SRX23527802,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30600,SRR27865239,SRX23527801,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,KDM4C MO,5,5,KDM4C MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,KDM-MO_1.fq.gz KDM-MO_2.fq.gz,fastq fastq,7876840500.0,26256135.0,KDM MO 1.fq.gz,0:150 1:150,A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469,150,150,,,2104173142,1831662159,1843980192,2096831538,193469,SRX23527801,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30601,SRR27865240,SRX23527800,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,ZNF662 MO,4,4,ZNF662 MO,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,znf547-MO_1.fq.gz znf547-MO_2.fq.gz,fastq fastq,7573815300.0,25246051.0,znf547 MO 1.fq.gz,0:150 1:150,A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628,150,150,,,2014197761,1766587259,1782217029,2010540623,272628,SRX23527800,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30602,SRR27865241,SRX23527799,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,SEMA5A RNA,3,3,SEMA5A RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,semRNA_1.fq.gz semRNA_2.fq.gz,fastq fastq,5575566000.0,18585220.0,semRNA 1.fq.gz,0:150 1:150,A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165,150,150,,,1456001758,1325628099,1339796989,1454076989,62165,SRX23527799,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30603,SRR27865242,SRX23527798,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,MT ATP6 RNA,2,2,MT ATP6 RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz,fastq fastq,5437771200.0,18125904.0,ATP6 RNA 1.fq.gz,0:150 1:150,A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633,150,150,,,1438540045,1272310670,1290121053,1436739799,59633,SRX23527798,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
30604,SRR27865243,SRX23527797,SRS20377517,SRP488009,PRJNA1073183,Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos,PRJNA1073183,Other,,,,,Embryos transcriptome,Embryos transcriptome,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con RNA,1,1,con RNA,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP488009,,,con-RNA_1.fq.gz con-RNA_2.fq.gz,fastq fastq,6733158900.0,22443863.0,con RNA 1.fq.gz,0:150 1:150,A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220,150,150,,,1766014369,1595337569,1610127771,1761604971,74220,SRX23527797,SRS20377517,SRA1797184,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-02-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 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 x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000 R 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_BO623-04T0022_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,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 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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_BO623-04T0021_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,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 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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_BO623-04T0020_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,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 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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_BO623-04T0019_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,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 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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_BO623-04T0018_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,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 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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_BO623-04T0017_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,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 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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_BO623-04T0016_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,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 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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_BO623-04T0015_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,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 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 x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000 R 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_BO623-04T0024_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,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 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 x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000 R 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_BO623-04T0023_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,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,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 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 x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000  x0000 R 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_BO623-04T0013_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
33326,SRR29962931,SRX25444536,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,zx150 RNAseq,4,4,zx150 RNAseq,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,zx150_input_1.fq.gz zx150_input_2.fq.gz,fastq fastq,11540682300.0,38468941.0,zx150 input 1.fq.gz,0:150 1:150,A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003,150,150,,,3038586049,2720235923,2771004747,3010645578,210003,SRX25444536,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures
33327,SRR29962932,SRX25444535,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con RNAseq,3,3,con RNAseq,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz,fastq fastq,11610174300.0,38700581.0,con zx150 input 1.fq.gz,0:150 1:150,A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827,150,150,,,3049654977,2746004045,2795023766,3019280685,210827,SRX25444535,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures
33328,SRR29962933,SRX25444534,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,zx150 m6A,2,2,zx150 m6A,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,zx150_IP_1.fq.gz zx150_IP_2.fq.gz,fastq fastq,17410816801.0,80469610.0,zx150 IP 1.fq.gz,0:108.79 1:107.58,A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583,108,107,,,4434870667,3759430468,4812205613,4404166470,143583,SRX25444534,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures
33329,SRR29962934,SRX25444533,SRS22101407,SRP521963,PRJNA1139824,Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq,PRJNA1139824,Other,Toxicity of sine wave on early zebrafish embryo development,,,,Embryos m6A transcriptome,Embryos m6A transcriptome of SW,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal,,,,,,,,,con m6A,1,1,con m6A,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP521963,,,con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz,fastq fastq,16822889423.0,77865752.0,con zx150 IP 1.fq.gz,0:108.68 1:107.37,A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001,108,107,,,4324048234,3668630618,4601614069,4228151501,445001,SRX25444533,SRS22101407,SRA1931991,Sichuan University|West China Second University Hospital,Sichuan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-24,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36663,SRR800049,SRX257156,SRS405710,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,sphere RNAseq 5azaCyD control,,strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere,,,,,,,,,sphere RNAseq 5azaCyD control,sphere RNAseq 5azaCyD control,9323X2,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP020008,,,sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz,Illumina native,2563410950.0,51268219.0,9323X2 120628 SN141 0513 AD12CFACXX 4,0:50,A:663337120;C:603101927;G:752336300;T:542924123;N:1711480,50,,,,663337120,603101927,752336300,542924123,1711480,SRX257156,SRS405710,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.65713,,0.09976,,0.81677,,0.81063,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-05-07,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36664,SRR800046,SRX257155,SRS405709,SRP020008,PRJNA193544,Danio rerio strain:Tubingen Epigenomics,PRJNA193544,Other,Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.,,pubmed:23663776,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,Generic sample from Danio rerio,sphere RNAseq 5azaCyD treatment,,strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere,,,,,,,,,sphere RNAseq 5azaCyD treatment,sphere RNAseq 5azaCyD treatment,9323X1,1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP020008,,,sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz,Illumina native,2595654550.0,51913091.0,9323X1 120628 SN141 0513 AD12CFACXX 4,0:50,A:676999669;C:618386951;G:759497082;T:539035799;N:1735049,50,,,,676999669,618386951,759497082,539035799,1735049,SRX257155,SRS405709,SRA072148,University of Utah|Brad Cairns Lab,University of Utah,1,0.76926,,0.12287,,0.82408,,0.72244,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,United States,2013-04-03,Blastula,Embryo,Embryo Imprecise,All anatomical structures
36695,SRR831692,SRX269410,SRS415075,SRP021210,PRJNA197389,Danio rerio strain:Wildtype strains AB  WIK  and AB/Tueb Transcriptome or Gene expression,PRJNA197389,Transcriptome Analysis,Gene expression profiling of several wildtype strains of zebrafish embryos. The samples were pooled from several developmental stages ranging from 2 dpf to 7 dpf This breadth of sampling gives a broad idea of genes expressed during early development and SNPs associated with wildtype strains.,,pubmed:23299976,,RNA seq from Fred Hutchinscon AB strain of Danio rerio,AB FH.bam,,geo loc name:USA: Seattle  WA|isolation source:zebrafish embryos|subspecf gen lin:AB from Fred Hutchinson|dev stage:mix of 2 dpf 7 dpf type:pool of multiple embryos from each develomental stage|strain:AB,,,,,,,,,AB FH,AB FH,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP021210,,,FH_AB.bam,bam,2246623442.0,24070720.0,AB FH,0:49 1:49,A:574600075;C:551290408;G:541354340;T:579331239;N:47380,49,49,,,574600075,551290408,541354340,579331239,47380,SRX269410,SRS415075,SRA073810,Fred Hutchinson Cancer Research Center|Moens,Fred Hutchinson Cancer Research Center,2,0.96858,0.96855,0.08369,0.08397,0.67953,0.67959,0.45983,0.44926,49,49,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2014-04-19,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
42451,SRR5590336,SRX2847138,SRS2220119,SRP115073,PRJNA387549,zebrafish Raw sequence reads,PRJNA387549,Metagenomics,The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.,,,,without xxx and with difenoconazole,CK D 50 D 500,,strain:AB|isolate:embryo|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:pooled male and female|tissue:whole individual|BioSampleModel:Model organism or animal,,,,,,,,,RNA Sequencing in zebrafish without xxx and with difenoconazole,zebrafish RNA Sequencing project,1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>6</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP115073,,,CK_1_1.fq.gz CK_1_2.fq.gz CK_2_1.fq.gz CK_3_1.fq.gz CK_3_2.fq.gz D_500_1_1.fq.gz D_500_1_2.fq.gz D_500_2_1.fq.gz D_500_2_2.fq.gz D_500_3_1.fq.gz D_500_3_2.fq.gz D_50_1_1.fq.gz D_50_1_2.fq.gz D_50_3_2.fq.gz D_50_3_1.fq.gz D_50_2_2.fq.gz D_50_2_1.fq.gz CK_2_2.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,81797448900.0,272658163.0,zebrafish RNA Seq,0:150 1:150,A:21743331485;C:19042575463;G:19378823851;T:21630253992;N:2464109,150,150,,,21743331485,19042575463,19378823851,21630253992,2464109,SRX2847138,SRS2220119,SRA564978,China Agricultural University|College of Science,China Agricultural University,2,0.91941,0.92018,0.10515,0.10533,0.67939,0.68552,0.46739,0.46494,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-04-14,Undetermined,Embryo,Whole Organism,All anatomical structures
43660,SRR6003528,SRX3158823,SRS2490160,SRP116760,PRJNA401346,Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos,PRJNA401346,Other,To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.,,,100 embyos micorinjected with morphorlinos of miR 462,Danio rerio embryos,462MO 48hpf,,strain:AB|dev stage:48hpf|sex:not applicable|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:micorinjected with morphorlinos of miR 462|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: 48hpf embryos,462MO 48hpf,462MO 48hpf,Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer¡¯s recommendations and indexcodes were added to attribute sequences to each sample.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP116760,,,,,3643659000.0,14574636.0,M462MO48 1.fq.gz,0:125 1:125,A:929370426;C:890981335;G:907736720;T:914809265;N:761254,125,125,,,929370426,890981335,907736720,914809265,761254,SRX3158823,SRS2490160,SRA605241,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.94745,0.94585,0.03062,0.0299,0.71005,0.7167,0.47212,0.46832,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,nebnext,bulk,unknown,unknown,,China,2017-09-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
43661,SRR6003529,SRX3158822,SRS2490159,SRP116760,PRJNA401346,Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos,PRJNA401346,Other,To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.,,,100 embyos of uninjected control,Danio rerio embryos,Control 48hpf,,strain:AB|dev stage:48hpf|sex:not applicable|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:uninjected control|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: 48hpf embryos,Control 48hpf,Control 48hpf,Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer¡¯s recommendations and indexcodes were added to attribute sequences to each sample.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP116760,,,,,3723608000.0,14894432.0,Contr48 2.fq.gz,0:125 1:125,A:947710287;C:910496767;G:932389849;T:932231152;N:779945,125,125,,,947710287,910496767,932389849,932231152,779945,SRX3158822,SRS2490159,SRA605241,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.94491,0.94085,0.0282,0.02794,0.70928,0.71636,0.46153,0.4685,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,nebnext,bulk,unknown,unknown,,China,2017-09-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
43662,SRR6003530,SRX3158821,SRS2490158,SRP116760,PRJNA401346,Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos,PRJNA401346,Other,To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.,,,100 embyos micorinjected with morphorlinos of miR 731,Danio rerio embryos,731MO 48hpf,,strain:AB|dev stage:48hpf|sex:not determined|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:micorinjected with morphorlinos of miR 731|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish: 48hpf embryos,731MO 48hpf,731MO 48hpf,Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer¡¯s recommendations and indexcodes were added to attribute sequences to each sample.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP116760,,,,,3700848750.0,14803395.0,M731MO48 2.fq.gz,0:125 1:125,A:939687783;C:909029785;G:925521644;T:925836207;N:773331,125,125,,,939687783,909029785,925521644,925836207,773331,SRX3158821,SRS2490158,SRA605241,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.94623,0.94506,0.02919,0.02927,0.71583,0.72342,0.47105,0.47193,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,nebnext,bulk,unknown,unknown,,China,2017-09-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
47607,SRR6996532,SRX3931184,SRS3164482,SRP137031,PRJNA432757,zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage,PRJNA432757,Other,To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.,,,,maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 2,marcksbMZ shield rep2,,strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 2,MZmarcksb shield PE150 rep2,MZmarcksb shield PE150 rep2,The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP137031,,,marcksbMZ2_shield_R1.fastq.bz2 marcksbMZ2_shield_R2.fastq.bz2,fastq fastq,957075410.0,3388133.0,marcksbMZ2 shield R2.fastq.bz2,0:141.21 1:141.27,A:252634407;C:225426820;G:225127111;T:253882486;N:4586,141,141,,,252634407,225426820,225127111,253882486,4586,SRX3931184,SRS3164482,SRA688612,"Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.9602,0.96488,0.04777,0.04815,0.76753,0.7697,0.48813,0.4867,150,151,B,B,biological fallback assumption,illumina,miseq,unknown,other,trueseq,bulk,unknown,unknown,,China,2018-04-12,Gastrula,Embryo,Whole Organism,All anatomical structures
47608,SRR6996479,SRX3931150,SRS3164467,SRP137031,PRJNA432757,zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage,PRJNA432757,Other,To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.,,,,maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 1,marcksbMZ shield rep1,,strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 1,MZmarcksb shield PE150 rep1,MZmarcksb shield PE150 rep1,The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP137031,,,marcksbMZ1_shield_R2.fastq.bz2 marcksbMZ1_shield_R1.fastq.bz2,fastq fastq,1298313857.0,4880467.0,marcksbMZ1 shield R2.fastq.bz2,0:132.94 1:133.09,A:343658239;C:305189492;G:304679186;T:344779644;N:7296,132,133,,,343658239,305189492,304679186,344779644,7296,SRX3931150,SRS3164467,SRA688589,"Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.95673,0.96117,0.05347,0.05421,0.76751,0.76936,0.48125,0.48179,130,130,B,B,biological fallback assumption,illumina,miseq,unknown,other,trueseq,bulk,unknown,unknown,,China,2018-04-12,Gastrula,Embryo,Whole Organism,All anatomical structures
47609,SRR6987273,SRX3926781,SRS3160495,SRP137031,PRJNA432757,zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage,PRJNA432757,Other,To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.,,,,WT whole embryos at shield stage from Danio rerio,WT1 shield,,strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: WT embryos at shield stage replicate 2,wt shield PE rep2,wt shield PE rep2,The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina MiSeq,,SRP137031,,,WT2_shield_R1.fastq.bz2 WT2_shield_R2.fastq.bz2,fastq fastq,1076081986.0,3852554.0,WT2 shield R1.fastq.bz2,0:139.62 1:139.70,A:280164367;C:257377429;G:257794541;T:280730273;N:15376,139,139,,,280164367,257377429,257794541,280730273,15376,SRX3926781,SRS3160495,SRA687978,"Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.93567,0.94244,0.04042,0.04049,0.77455,0.77697,0.48487,0.47998,151,151,B,B,biological fallback assumption,illumina,miseq,unknown,other,trueseq,bulk,unknown,unknown,,China,2018-04-12,Gastrula,Embryo,Whole Organism,All anatomical structures
47610,SRR6933827,SRX3878878,SRS3118690,SRP137031,PRJNA432757,zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage,PRJNA432757,Other,To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.,,,,,WT1 shield rep1,,strain:AB|dev stage:shield stage|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: WT embryos at shield stage replicate 1,wt shield PE rep1,wt shield PE rep1,The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,NextSeq 500,,SRP137031,,,WT1_shield_R1.fastq.bz2 WT1_shield_R2.fastq.bz2,fastq fastq,892273276.0,3407597.0,WT1 shield R1.fastq.bz2,0:130.75 1:131.10,A:235694986;C:210056075;G:210344332;T:236174033;N:3850,130,131,,,235694986,210056075,210344332,236174033,3850,SRX3878878,SRS3118690,SRA681078,"Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio","Institute of Hydrobiology, Chinese Academy of Sciences",2,0.95143,0.95581,0.04389,0.04405,0.77143,0.77319,0.48336,0.48263,118,118,B,B,biological fallback assumption,illumina,nextseq,unknown,other,trueseq,bulk,unknown,unknown,,China,2018-04-03,Gastrula,Embryo,Whole Organism,All anatomical structures
51069,SRR8926593,SRX5707650,SRS4646935,SRP192957,PRJNA515990,zebrafish miR 430 KO transcriptome,PRJNA515990,Other,MiR 430 is considered an important regulator during embryonic development  but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement  germ layer specification  axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets  we collected the WT  miR 430 /  and rescued embryos at shield stage and performed transcriptome sequencing.,,,miR 430 /  embryos were injected with miR 430 rescued  20 embryos at shield stage were collected for RNA seq analsysis,Rescued,R6,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:Rescued by miR 430 injection|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish miR 430 KO,5065335,5065335,high throughtput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP192957,,,R6_GTGGCC_L001_R1_001.fastq.gz R6_GTGGCC_L001_R2_001.fastq.gz R6_GTGGCC_L002_R1_001.fastq.gz R6_GTGGCC_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3784504800.0,18922524.0,R6 GTGGCC L001 R1 001.fastq.gz,0:100 1:100,A:998174818;C:911994688;G:866970560;T:1007223918;N:140816,100,100,,,998174818,911994688,866970560,1007223918,140816,SRX5707650,SRS4646935,SRA876443,Sun Yat-Sen University|School of Life Sciences,Sun Yat-Sen University,2,0.95548,0.95511,0.07794,0.079,0.75603,0.75933,0.48812,0.48112,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-04-18,Gastrula,Embryo,Whole Organism,All anatomical structures
51070,SRR8926594,SRX5707649,SRS4646934,SRP192957,PRJNA515990,zebrafish miR 430 KO transcriptome,PRJNA515990,Other,MiR 430 is considered an important regulator during embryonic development  but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement  germ layer specification  axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets  we collected the WT  miR 430 /  and rescued embryos at shield stage and performed transcriptome sequencing.,,,20 miR 430 /  embryos at shield stage were collected for RNA seq analsysis,MiR 430 / ,M6,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:miR 430 was deleted by TALENs|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish miR 430 KO,5065334,5065334,high throughtput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP192957,,,M6_GTGAAA_L002_R2_001.fastq.gz M6_GTGAAA_L002_R1_001.fastq.gz M6_GTGAAA_L001_R2_001.fastq.gz M6_GTGAAA_L001_R1_001.fastq.gz,fastq fastq fastq fastq,3957356200.0,19786781.0,M6 GTGAAA L001 R1 001.fastq.gz,0:100 1:100,A:1047013756;C:951740713;G:905354408;T:1053098995;N:148328,100,100,,,1047013756,951740713,905354408,1053098995,148328,SRX5707649,SRS4646934,SRA876443,Sun Yat-Sen University|School of Life Sciences,Sun Yat-Sen University,2,0.9588,0.95721,0.07699,0.07822,0.75422,0.75903,0.47996,0.48477,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-04-18,Gastrula,Embryo,Whole Organism,All anatomical structures
51071,SRR8926595,SRX5707648,SRS4646933,SRP192957,PRJNA515990,zebrafish miR 430 KO transcriptome,PRJNA515990,Other,MiR 430 is considered an important regulator during embryonic development  but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement  germ layer specification  axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets  we collected the WT  miR 430 /  and rescued embryos at shield stage and performed transcriptome sequencing.,,,20 WT embryos at shield stage were collected for RNA seq analsysis,WT,W6,,strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:WT|sample type:embryos|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish miR 430 KO,5065333,5065333,high throughtput sequencing,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP192957,,,W6_GTCCGC_L001_R2_001.fastq.gz W6_GTCCGC_L002_R1_001.fastq.gz W6_GTCCGC_L002_R2_001.fastq.gz W6_GTCCGC_L001_R1_001.fastq.gz,fastq fastq fastq fastq,3409986400.0,17049932.0,W6 GTCCGC L001 R1 001.fastq.gz,0:100 1:100,A:898095172;C:823280875;G:782808699;T:905676163;N:125491,100,100,,,898095172,823280875,782808699,905676163,125491,SRX5707648,SRS4646933,SRA876443,Sun Yat-Sen University|School of Life Sciences,Sun Yat-Sen University,2,0.95598,0.95417,0.07794,0.07924,0.76063,0.7627,0.47632,0.47729,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-04-18,Gastrula,Embryo,Whole Organism,All anatomical structures
55296,SRR10394606,SRX7094986,SRS5607478,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case2 3,,sample title for replicate:2 3|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,case2 3,2 3,2 3,To screen differential expression genes in zebrafish following BPF exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case2-3_HGLWJALXX_L3_1.fq.gz 170296A-case2-3_HGLWJALXX_L3_2.fq.gz,fastq fastq,8855015700.0,29516719.0,170296A case2 3 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2346373651;C:2080129725;G:2086423043;T:2340561908;N:1527373,150,150,,,2346373651,2080129725,2086423043,2340561908,1527373,SRX7094986,SRS5607478,SRA990382,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93245,0.93174,0.09246,0.09206,0.65147,0.66393,0.47376,0.47499,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55297,SRR10394607,SRX7094985,SRS5607477,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case2 2,,sample title for replicate:2 2|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,case2 2,2 2,2 2,To screen differential expression genes in zebrafish following BPF exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case2-2_HGLWJALXX_L3_1.fq.gz 170296A-case2-2_HGLWJALXX_L3_2.fq.gz,fastq fastq,9061419900.0,30204733.0,170296A case2 2 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2400908650;C:2127711127;G:2137324991;T:2393913073;N:1562059,150,150,,,2400908650,2127711127,2137324991,2393913073,1562059,SRX7094985,SRS5607477,SRA990382,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.9283,0.92706,0.09788,0.09751,0.65407,0.66174,0.47665,0.46756,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55298,SRR10394608,SRX7094984,SRS5607476,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case2 1,,sample title for replicate:2 1|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,case2 1,2 1,2 1,To screen differential expression genes in zebrafish following BPF exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case2-1_HGLWJALXX_L3_1.fq.gz 170296A-case2-1_HGLWJALXX_L3_2.fq.gz,fastq fastq,7957722900.0,26525743.0,170296A case2 1 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2091268133;C:1885173791;G:1895292430;T:2084598568;N:1389978,150,150,,,2091268133,1885173791,1895292430,2084598568,1389978,SRX7094984,SRS5607476,SRA990382,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93071,0.93062,0.09541,0.09537,0.66218,0.67343,0.44795,0.45757,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55299,SRR10394609,SRX7094983,SRS5607475,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,con3,,sample title for replicate:0 3|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,con3,0 3,0 3,To screen differential expression genes in zebrafish following BPF exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-con-3_HGLWJALXX_L3_1.fq.gz 170296A-con-3_HGLWJALXX_L3_2.fq.gz,fastq fastq,8887815900.0,29626053.0,170296A con 3 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2352143987;C:2092070321;G:2106757875;T:2335298934;N:1544783,150,150,,,2352143987,2092070321,2106757875,2335298934,1544783,SRX7094983,SRS5607475,SRA990382,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92657,0.92558,0.10953,0.10849,0.66665,0.67836,0.46528,0.46952,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55300,SRR10394610,SRX7094982,SRS5505505,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,con2,,sample title for replicate:0 2|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,con2,0 2,0 2,To screen differential expression genes in zebrafish following BPF exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-con-2_HGLWJALXX_L3_1.fq.gz 170296A-con-2_HGLWJALXX_L3_2.fq.gz,fastq fastq,9166144200.0,30553814.0,170296A con 2 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2412585744;C:2169053726;G:2180991082;T:2401934095;N:1579553,150,150,,,2412585744,2169053726,2180991082,2401934095,1579553,SRX7094982,SRS5505505,SRA990382,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93019,0.92958,0.09201,0.0912,0.65202,0.66247,0.4734,0.45718,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-05,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55301,SRR10267094,SRX6980545,SRS5505504,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,con1,,sample title for replicate:0 1|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 1,0 1,0 1,zebrafish embryo samples,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-con-1_HGLWJALXX_L3_1.fq.gz 170296A-con-3_HGLWJALXX_L3_2.fq.gz,fastq fastq,9415458300.0,31384861.0,170296A con 1 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2474617601;C:2231195853;G:2241864685;T:2466146702;N:1633459,150,150,,,2474617601,2231195853,2241864685,2466146702,1633459,SRX6980545,SRS5505504,SRA977706,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93028,0.92841,0.09571,0.09503,0.65746,0.66543,0.47028,0.46071,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-10-11,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55302,SRR10267095,SRX6980544,SRS5505503,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case1 3,,sample title for replicate:1 3|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,1 3,1 3,1 3,zebrafish embryo samples,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case1-3_HGLWJALXX_L4_1.fq.gz 170296A-case2-3_HGLWJALXX_L4_2.fq.gz,fastq fastq,7223133300.0,24077111.0,170296A case1 3 HGLWJALXX L4 1.fq.gz,0:150 1:150,A:1925695574;C:1683782909;G:1684865390;T:1928620280;N:169147,150,150,,,1925695574,1683782909,1684865390,1928620280,169147,SRX6980544,SRS5505503,SRA977706,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92712,0.92938,0.10141,0.10152,0.65206,0.65924,0.46219,0.46826,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-10-11,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55303,SRR10267096,SRX6980543,SRS5505502,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case1 2,,sample title for replicate:1 2|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,1 2,1 2,1 2,zebrafish embryo samples,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case2-2_HGLWJALXX_L3_2.fq.gz 170296A-case1-2_HGLWJALXX_L3_1.fq.gz,fastq fastq,9322039500.0,31073465.0,170296A case1 2 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2480808882;C:2178450729;G:2189618007;T:2471557593;N:1604289,150,150,,,2480808882,2178450729,2189618007,2471557593,1604289,SRX6980543,SRS5505502,SRA977706,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93046,0.92939,0.10201,0.10148,0.65417,0.66182,0.46825,0.47199,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-10-11,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55304,SRR10267097,SRX6980542,SRS5505501,SRP225201,PRJNA576995,RNA sequencing for differential expression gene screening in zebrafish,PRJNA576995,Other,To screen differential expression genes in zebrafish following BPF exposure,,,,,case1 1,,sample title for replicate:1 1|strain:not applicable|age:48 hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,1 1,1 1,1 1,zebrafish embryo samples,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP225201,,,170296A-case1-1_HGLWJALXX_L3_1.fq.gz 170296A-case2-1_HGLWJALXX_L3_2.fq.gz,fastq fastq,9593332800.0,31977776.0,170296A case1 1 HGLWJALXX L3 1.fq.gz,0:150 1:150,A:2527044547;C:2268335173;G:2277186987;T:2519119012;N:1647081,150,150,,,2527044547,2268335173,2277186987,2519119012,1647081,SRX6980542,SRS5505501,SRA977706,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93213,0.93298,0.09449,0.09434,0.65772,0.66596,0.46597,0.46237,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-10-11,Hatching,Embryo,Embryo Imprecise,All anatomical structures
55465,SRR10425371,SRX7121468,SRS5631400,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DBP 3,,sample title for replicate:2 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DBP 3,2 3,2 3,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DBP_3_S11_L001_R1_001.fastq.gz 160653A_DBP_3_S11_L001_R2_001.fastq.gz 160653A_DBP_3_S11_L002_R1_001.fastq.gz 160653A_DBP_3_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,4213944331.0,16837823.0,160653A DBP 3 S11 L001 R1 001.fastq.gz,0:125.11 1:125.16,A:1140267822;C:951856511;G:956555719;T:1143228000;N:22036279,125,125,,,1140267822,951856511,956555719,1143228000,22036279,SRX7121468,SRS5631400,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92075,0.92322,0.13421,0.13417,0.66884,0.67131,0.46585,0.45982,125,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55466,SRR10425372,SRX7121467,SRS5631399,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DBP 2,,sample title for replicate:2 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DBP 2,2 2,2 2,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DBP_2_S23_L002_R1_001.fastq.gz 160653A_DBP_2_S23_L002_R2_001.fastq.gz,fastq fastq,983641304.0,3925939.0,160653A DBP 2 S23 L002 R1 001.fastq.gz,0:125.26 1:125.29,A:263874385;C:226824475;G:226589811;T:265169405;N:1183228,125,125,,,263874385,226824475,226589811,265169405,1183228,SRX7121467,SRS5631399,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93403,0.93521,0.12516,0.12672,0.66596,0.66815,0.46015,0.46602,126,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55467,SRR10425373,SRX7121466,SRS5631398,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DBP 1,,sample title for replicate:2 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DBP 1,2 1,2 1,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DBP_1_S10_L001_R1_001.fastq.gz 160653A_DBP_1_S10_L001_R2_001.fastq.gz 160653A_DBP_1_S10_L002_R1_001.fastq.gz 160653A_DBP_1_S10_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3902022384.0,15589553.0,160653A DBP 1 S10 L001 R1 001.fastq.gz,0:125.13 1:125.17,A:1041532695;C:895336677;G:897445748;T:1047319053;N:20388211,125,125,,,1041532695,895336677,897445748,1047319053,20388211,SRX7121466,SRS5631398,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92278,0.92593,0.12212,0.12242,0.66381,0.66653,0.46732,0.46157,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55468,SRR10425374,SRX7121465,SRS5631397,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DEHP 3,,sample title for replicate:1 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DEHP 3,1 3,1 3,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DEHP_3_S9_L001_R1_001.fastq.gz 160653A_DEHP_3_S9_L001_R2_001.fastq.gz 160653A_DEHP_3_S9_L002_R1_001.fastq.gz 160653A_DEHP_3_S9_L002_R2_001.fastq.gz,fastq fastq fastq fastq,3978190342.0,15890841.0,160653A DEHP 3 S9 L001 R1 001.fastq.gz,0:125.15 1:125.19,A:1057764550;C:917477196;G:923586377;T:1058742562;N:20619657,125,125,,,1057764550,917477196,923586377,1058742562,20619657,SRX7121465,SRS5631397,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92571,0.92902,0.11691,0.11736,0.67192,0.67383,0.46273,0.46475,125,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55469,SRR10425375,SRX7121464,SRS5631396,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DEHP 2,,sample title for replicate:1 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DEHP 2,1 2,1 2,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DEHP_2_S22_L002_R1_001.fastq.gz 160653A_DEHP_2_S22_L002_R2_001.fastq.gz,fastq fastq,925063432.0,3692039.0,160653A DEHP 2 S22 L002 R1 001.fastq.gz,0:125.26 1:125.30,A:247171641;C:214421668;G:215124515;T:247261313;N:1084295,125,125,,,247171641,214421668,215124515,247261313,1084295,SRX7121464,SRS5631396,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93712,0.93841,0.12004,0.12183,0.67231,0.6747,0.47057,0.46379,124,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55470,SRR10425376,SRX7121463,SRS5631395,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,DEHP 1,,sample title for replicate:1 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,DEHP 1,1 1,1 1,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_DEHP_1_S8_L001_R1_001.fastq.gz 160653A_DEHP_1_S8_L001_R2_001.fastq.gz 160653A_DEHP_1_S8_L002_R1_001.fastq.gz 160653A_DEHP_1_S8_L002_R2_001.fastq.gz,fastq fastq fastq fastq,4181311851.0,16698140.0,160653A DEHP 1 S8 L001 R1 001.fastq.gz,0:125.19 1:125.22,A:1132179802;C:946301758;G:946478272;T:1135074674;N:21277345,125,125,,,1132179802,946301758,946478272,1135074674,21277345,SRX7121463,SRS5631395,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92101,0.92416,0.13798,0.13866,0.6678,0.66963,0.46137,0.46314,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55471,SRR10425377,SRX7121462,SRS5631394,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,con 3,,sample title for replicate:0 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,con 3,0 3,0 3,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_con_3_S7_L002_R2_001.fastq.gz 160653A_con_3_S7_L002_R1_001.fastq.gz 160653A_con_3_S7_L001_R2_001.fastq.gz 160653A_con_3_S7_L001_R1_001.fastq.gz,fastq fastq fastq fastq,4645800774.0,18572727.0,160653A con 3 S7 L001 R1 001.fastq.gz,0:125.05 1:125.09,A:1251751873;C:1054269377;G:1062381476;T:1252233640;N:25164408,125,125,,,1251751873,1054269377,1062381476,1252233640,25164408,SRX7121462,SRS5631394,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.9211,0.92397,0.13775,0.13782,0.6703,0.6728,0.46466,0.46374,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55472,SRR10425378,SRX7121461,SRS5631393,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,con 2,,sample title for replicate:0 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,con 2,0 2,0 2,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_con_2_S108_L008_R1_001.fastq.gz 160653A_con_2_S108_L008_R2_001.fastq.gz,fastq fastq,752863995.0,3006358.0,160653A con 2 S108 L008 R1 001.fastq.gz,0:125.20 1:125.23,A:203171883;C:172318434;G:172771199;T:203551286;N:1051193,125,125,,,203171883,172318434,172771199,203551286,1051193,SRX7121461,SRS5631393,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.93253,0.93349,0.13528,0.13652,0.66186,0.66665,0.46382,0.47405,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
55473,SRR10425379,SRX7121460,SRS5631392,SRP229414,PRJNA588649,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,PRJNA588649,Other,,,,,,con 1,,sample title for replicate:0 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,con 1,0 1,0 1,RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP229414,,,160653A_con_1_S6_L001_R1_001.fastq.gz 160653A_con_1_S6_L001_R2_001.fastq.gz 160653A_con_1_S6_L002_R1_001.fastq.gz 160653A_con_1_S6_L002_R2_001.fastq.gz,fastq fastq fastq fastq,4387536203.0,17538394.0,160653A con 1 S6 L001 R1 001.fastq.gz,0:125.06 1:125.11,A:1178097571;C:999772360;G:1005888816;T:1180262110;N:23515346,125,125,,,1178097571,999772360,1005888816,1180262110,23515346,SRX7121460,SRS5631392,SRA993820,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,2,0.92006,0.92409,0.13074,0.13101,0.66263,0.66505,0.4728,0.47345,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-11-11,Larval,Larval,Embryo Imprecise,All anatomical structures
58872,SRR11510448,SRX8082500,SRS6450585,SRP255712,PRJNA623798,Single cell lineage tracing on endogenous scarring sites scLOESS,PRJNA623798,Other,Lineage recording of zebrafish embryogenesis reveals early cell fate commitment,,,The developmental history of a whole zebrafish organism were recording by LOESS Lineage tracing Of Endogenous Scarring Sites technique.  And both cell lineage histories and cell molecular profile were reconstructed by single cell RNA Seq profiling  with the help of single cell sequencing methods and self developed analysis strategies.,Single Cell RNA Seq of a whole organism of zebrafish larva,SC,,strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal,,,,,,,,,Single Cell RNA Seq of a whole organism of zebrafish larva,SC L3,SC L3,Zebrafish embryo at one cell stage were micro injected with gRNA pool and Cas9 mRNA mixture  and growth at standard condiction ttwo xxxdpf. Then a single larva were lysis into single cell suspension and the RNA profile were obtained by 10x Genomics Chromium Single Cell three prime Reagent Kits v2 Chemistry.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,RT-PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP255712,,,SC-I1_S1_L001_R1_001.fastq.gz SC-I1_S1_L001_R2_001.fastq.gz SC-I1_S1_L002_R1_001.fastq.gz SC-I1_S1_L002_R2_001.fastq.gz SC-I1_S1_L003_R1_001.fastq.gz SC-I1_S1_L003_R2_001.fastq.gz SC-I2_S1_L001_R1_001.fastq.gz SC-I2_S1_L001_R2_001.fastq.gz SC-I2_S1_L002_R1_001.fastq.gz SC-I2_S1_L002_R2_001.fastq.gz SC-I2_S1_L003_R1_001.fastq.gz SC-I2_S1_L003_R2_001.fastq.gz SC-I3_S1_L001_R1_001.fastq.gz SC-I3_S1_L001_R2_001.fastq.gz SC-I3_S1_L002_R1_001.fastq.gz SC-I3_S1_L002_R2_001.fastq.gz SC-I3_S1_L003_R1_001.fastq.gz SC-I3_S1_L003_R2_001.fastq.gz SC-I4_S1_L001_R1_001.fastq.gz SC-I4_S1_L001_R2_001.fastq.gz SC-I4_S1_L002_R1_001.fastq.gz SC-I4_S1_L002_R2_001.fastq.gz SC-I4_S1_L003_R1_001.fastq.gz SC-I4_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,86925323584.0,493893884.0,SC I1 S1 L001 R1 001.fastq.gz,0:26 1:150,A:24075189135;C:19816237204;G:21200277502;T:21828035227;N:5584516,26,150,,,24075189135,19816237204,21200277502,21828035227,5584516,SRX8082500,SRS6450585,SRA1063827,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.00528,0.77254,0.00115,0.06529,0.98729,0.8158,0.41854,0.50141,26,150,T,B,sc-like readlen,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,China,2020-04-11,Larval,Larval,Whole Organism,All anatomical structures
62799,SRR13381327,SRX9804263,SRS7988468,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 1,,sample title for replicate:c 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 1,c 1,c 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c1-R1.fq.gz.gz c1-R2.fq.gz.gz,fastq fastq,3188746630.0,21313115.0,c1 R1.fq.gz.gz,0:149.61,A:907108265;C:694245090;G:701033373;T:886334111;N:25791,149,,,,907108265,694245090,701033373,886334111,25791,SRX9804263,SRS7988468,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88484,,0.19252,,0.72153,,0.51441,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62800,SRR13381328,SRX9804262,SRS7988467,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 3,,sample title for replicate:b 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 3,b 3,b 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b3-R1.fq.gz.gz b3-R2.fq.gz.gz,fastq fastq,3410851764.0,22784502.0,b3 R1.fq.gz.gz,0:149.70,A:978915230;C:735962678;G:739687608;T:956258485;N:27763,149,,,,978915230,735962678,739687608,956258485,27763,SRX9804262,SRS7988467,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.90179,,0.18495,,0.71541,,0.52314,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62801,SRR13381329,SRX9804261,SRS7988466,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 2,,sample title for replicate:b 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 2,b 2,b 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b2-R1.fq.gz.gz b2-R2.fq.gz.gz,fastq fastq,3152478044.0,21115710.0,b2 R1.fq.gz.gz,0:149.30,A:947002080;C:630086332;G:638703847;T:936677512;N:8273,149,,,,947002080,630086332,638703847,936677512,8273,SRX9804261,SRS7988466,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.80951,,0.24776,,0.77906,,0.57691,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62802,SRR13381330,SRX9804260,SRS7988465,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,b 1,,sample title for replicate:b 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,b 1,b 1,b 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,b1-R1.fq.gz.gz b1-R2.fq.gz.gz,fastq fastq,3352598587.0,22415585.0,b1 R1.fq.gz.gz,0:149.57,A:976446828;C:708370059;G:713539822;T:954214882;N:26996,149,,,,976446828,708370059,713539822,954214882,26996,SRX9804260,SRS7988465,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.90048,,0.22988,,0.71216,,0.4927,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62803,SRR13381331,SRX9804259,SRS7988464,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 3,,sample title for replicate:a 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 3,a 3,a 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a3-R1.fq.gz.gz a3-R2.fq.gz.gz,fastq fastq,3171167510.0,21201111.0,a3 R1.fq.gz.gz,0:149.58,A:904575002;C:687927904;G:693921563;T:884717279;N:25762,149,,,,904575002,687927904,693921563,884717279,25762,SRX9804259,SRS7988464,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87972,,0.19211,,0.73001,,0.51068,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62804,SRR13381332,SRX9804258,SRS7988463,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 2,,sample title for replicate:a 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 2,a 2,a 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a2-R1.fq.gz.gz a2-R2.fq.gz.gz,fastq fastq,2970077328.0,19894385.0,a2 R1.fq.gz.gz,0:149.29,A:877143980;C:609672974;G:615339733;T:867912969;N:7672,149,,,,877143980,609672974,615339733,867912969,7672,SRX9804258,SRS7988463,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.83922,,0.22546,,0.78386,,0.66266,,128,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62805,SRR13381333,SRX9804257,SRS7988462,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,a 1,,sample title for replicate:a 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,a 1,a 1,a 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,a1-R1.fq.gz.gz a1-R2.fq.gz.gz,fastq fastq,3355906399.0,22420666.0,a1 R1.fq.gz.gz,0:149.68,A:967471134;C:715589495;G:719383048;T:953453855;N:8867,149,,,,967471134,715589495,719383048,953453855,8867,SRX9804257,SRS7988462,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88569,,0.2199,,0.71486,,0.4934,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62806,SRR13381334,SRX9804256,SRS7988461,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 3,,sample title for replicate:0 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 3,0 3,0 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck3-R1.fq.gz.gz ck3-R2.fq.gz.gz,fastq fastq,3338640528.0,22323417.0,ck3 R1.fq.gz.gz,0:149.56,A:950056740;C:724127980;G:729397822;T:935049323;N:8663,149,,,,950056740,724127980,729397822,935049323,8663,SRX9804256,SRS7988461,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.8797,,0.17422,,0.72092,,0.50968,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62807,SRR13381335,SRX9804255,SRS7988460,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 3,,sample title for replicate:c 3|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 3,c 3,c 3,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c3-R1.fq.gz.gz c3-R2.fq.gz.gz,fastq fastq,3306682837.0,22088500.0,c3 R1.fq.gz.gz,0:149.70,A:931414367;C:728984036;G:734931077;T:911326441;N:26916,149,,,,931414367,728984036,734931077,911326441,26916,SRX9804255,SRS7988460,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.88469,,0.16886,,0.72308,,0.50922,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62808,SRR13381336,SRX9804254,SRS7988459,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,c 2,,sample title for replicate:c 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,c 2,c 2,c 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,c2-R1.fq.gz.gz c2-R2.fq.gz.gz,fastq fastq,3445029375.0,23065463.0,c2 R1.fq.gz.gz,0:149.36,A:1033514432;C:696726296;G:699357939;T:1015389477;N:41231,149,,,,1033514432,696726296,699357939,1015389477,41231,SRX9804254,SRS7988459,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87331,,0.30599,,0.72671,,0.54303,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62809,SRR13381337,SRX9804253,SRS7988458,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 2,,sample title for replicate:0 2|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 2,0 2,0 2,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck2-R1.fq.gz ck2-R2.fq.gz,fastq fastq,3311324763.0,22134043.0,ck2 R1.fq.gz,0:149.60,A:979349608;C:681079542;G:688681630;T:962205302;N:8681,149,,,,979349608,681079542,688681630,962205302,8681,SRX9804253,SRS7988458,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.87651,,0.27982,,0.71821,,0.51125,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
62810,SRR13381338,SRX9804252,SRS7988457,SRP300825,PRJNA690592,Transcriptomic of zebrafish embryos at 48 hpf,PRJNA690592,Other,,,,,,0 1,,sample title for replicate:0 1|strain:wild type|dev stage:embryonic|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,0 1,0 1,0 1,RT PCR,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP300825,,,ck1-R1.fq.gz ck1-R2.fq.gz,fastq fastq,3233079806.0,21640984.0,ck1 R1.fq.gz,0:149.40,A:929185111;C:690348531;G:699157160;T:914380522;N:8482,149,,,,929185111,690348531,699157160,914380522,8482,SRX9804252,SRS7988457,SRA1181496,Chinese academy of fishery sciences|fishery Resource and Environmental Research Center,Chinese academy of fishery sciences,1,0.86295,,0.20583,,0.7208,,0.52194,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2021-01-07,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
67034,SRR16991903,SRX13182261,SRS11111533,SRP347063,PRJNA782235,Nano Palladium free transcriptomic analysis in a non human model organism  Danio rerio,PRJNA782235,Other,The effects of free nano palladium in zebrafish  Danio rerio  was determined using transcriptome sequencing. The purity of mRNA from the control fishes were checked and the processed reads were mapped with the reference genome of Danio rerio. Around 67835 genes were expressed in control with respect to the total reads. The expressed genes showed no changes in their behaviour which is evident that the fishes without xxx exposure of xenobiotics caused no changes.,,,,,BUANControl,,strain:AB strain  Wild type|age:6 month|dev stage:adult|sex:male|tissue:Whole fish tissue|collection date:2021 03 06|store cond:Liquid Nitrogen|treatment:Nil|BioSampleModel:Model organism or animal,,,,,,,,,NP free study on Zebrafish,C1 Control NPfree Zebrafish,C1 Control NPfree Zebrafish,Palladium nanoparticles Pd NPs have been the reliable substitutes as conventional catalysts for its high efficiency and conversion of CO  hydrocarbons  and NO into less harmful CO2  water and nitrogen. Due to surface abrasion of converters  Pd as ultrafine/nanoparticles are liberated into the environment causing possible health effects. Also  Pd might reach the aquatic system through heavy precipitation and runoff. Here  we aimed to profile the transcriptome of Danio rerio exposed to nano palladium at environmentally relevant concentrations with control. 500 ng of total RNA of nano Pd free fishes Control was isolated and the enriched mRNAs were reverse transcribed to form cDNA. The purified amplified cDNA library was eluted in the TE buffer. The concentrations above 2 ng/µL were used for the transcriptome analysis with the reference genome. In the control group  67835 genes were expressed which showed no changes in their behavior.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP347063,,,Control_R1.fastq Control_R2.fastq,fastq fastq,4526842200.0,15089474.0,Control R1.fastq,0:150 1:150,A:1257431594;C:1009220672;G:1028452096;T:1231606739;N:131099,150,150,,,1257431594,1009220672,1028452096,1231606739,131099,SRX13182261,SRS11111533,SRA1332407,Bharathiar University|Zoology,Bharathiar University,2,0.84019,0.84256,0.12963,0.12905,0.70266,0.70761,0.54173,0.54265,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,India,2021-11-21,Adult,Adult,Whole Organism,All anatomical structures
67036,SRR17001172,SRX13191392,SRS11119484,SRP347216,PRJNA782554,Transcriptome profiling of environmental relevant low concentrations 0.4 ng/L of nano Palladium in Danio rerio,PRJNA782554,Other,The effects of nano palladium 0.4 ng per L in zebrafish  Danio rerio  was determined using transcriptome sequencing. The purity of mRNA from the control and nano Pd exposed fishes were checked and the processed reads were mapped with the reference genome of Danio rerio. Around 64792 genes were expressed in Treatment II respectively with respect to the total reads. There were 3153 differentially expressed genes in Control vs Treatment II with 2900 up regulated and 253 down regulated genes. Also  for Treatment I vs Treatment II  3347 genes were significantly differentially expressed with 2101 up regulated and 1246 down regulated genes. The up regulation and down regulation of the genes were evident that the nano Pd can affect the physiological and endocrine functions of zebrafish.,,,,,BUANNPd0.4ng,,strain:AB strain Wild Type|age:6 mpf|dev stage:Adult|sex:male|tissue:Whole Fish Tissue|collection date:2021 03 06|store cond:Liquid Nitrogen|treatment:0.4 ng/L nano Palladium|BioSampleModel:Model organism or animal,,,,,,,,,0.4 ng/L nano Pd exposed Zebrafish,nano Pd0.4ng,nano Pd0.4ng,Palladium nanoparticles Pd NPs have been the reliable substitutes as conventional catalysts for its high efficiency and conversion of CO  hydrocarbons  and NO into less harmful CO2  water and nitrogen. Due to surface abrasion of converters  Pd as ultrafine/nanoparticles are liberated into the environment causing possible health effects. Also  Pd leaches to the aquatic system through heavy precipitation and runoff. Here  we aimed to profile the transcriptome of Danio rerio exposed to nano palladium at xxx.4 ng/L environmental concentration. 500 ng of total RNA of 0.4 ng/L nano Pd fish was isolated and the enriched mRNAs were reverse transcribed to form cDNA. The concentrations above 2 ng/L were used for the transcriptome analysis with the reference genome. Around 64792 genes were expressed in 0.4 ng/L. There were 3153 DEGs in Control vs 0.4 ng/L with 2900 up regulated and 253 down regulated genes. Also  for 22 ng/L vs 0.4 ng/L  3347 genes were significantly expressed with 2101 up regulated and 1246 down regulated genes. The transcriptome screening is evident that nano Pd can cause possible effects in organisms even at low concentrations.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 1000,,SRP347216,,,Treated2_R1.fastq Treated2_R2.fastq,fastq fastq,4185717300.0,13952391.0,Treated2 R1.fastq,0:150 1:150,A:1131532349;C:966052110;G:976209681;T:1111787487;N:135673,150,150,,,1131532349,966052110,976209681,1111787487,135673,SRX13191392,SRS11119484,SRA1332836,ANILA P ASHOKAN|BHARATHIAR UNIVERSITY ZOOLOGY DEPARTEMNT,ANILA P ASHOKAN,2,0.90097,0.90521,0.05086,0.0512,0.71969,0.72403,0.45845,0.45942,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2021-11-22,Adult,Adult,Whole Organism,All anatomical structures
68542,SRR17994489,SRX14150133,SRS11975603,SRP359470,PRJNA806206,RNA seq for psip1a knockdown,PRJNA806206,Other,Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them  Psip1  the gene codes LEDGF/p75  has been implicated in cancer  autoimmune diseases and HIV pathogenesis. However  the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.,,,,,psip1aMO 3,,strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish embryos psip1a MO,psip1a MO3,psip1a MO3,The cDNA Library construction and quality control were coordinated by Novogen co.  Ltd,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP359470,,assembly:GRCz10,PSIP1AMO_experiment3_sorted.bam,bam,8445901500.0,28153005.0,PSIP1AMO experiment3 sorted.bam,0:150 1:150,A:2261122354;C:1981306733;G:1972898831;T:2230317126;N:256456,150,150,,,2261122354,1981306733,1972898831,2230317126,256456,SRX14150133,SRS11975603,SRA1370574,UC Merced|Bioengineering,UC Merced,2,0.94991,0.94968,0.08913,0.0893,0.68525,0.68621,0.46191,0.46633,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-02-11,Multi-stage,Embryo,Whole Organism,All anatomical structures
68543,SRR17994490,SRX14150132,SRS11975602,SRP359470,PRJNA806206,RNA seq for psip1a knockdown,PRJNA806206,Other,Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them  Psip1  the gene codes LEDGF/p75  has been implicated in cancer  autoimmune diseases and HIV pathogenesis. However  the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.,,,,,psip1aMO 2,,strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish embryos psip1a MO,psip1a MO2,psip1a MO2,The cDNA Library construction and quality control were coordinated by Novogen co.  Ltd,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP359470,,assembly:GRCz10,PSIP1AMO_experiment2_sorted.bam,bam,7506678900.0,25022263.0,PSIP1AMO experiment2 sorted.bam,0:150 1:150,A:1988273906;C:1776222092;G:1777720261;T:1964233379;N:229262,150,150,,,1988273906,1776222092,1777720261,1964233379,229262,SRX14150132,SRS11975602,SRA1370574,UC Merced|Bioengineering,UC Merced,2,0.95224,0.95202,0.07188,0.07212,0.68,0.6789,0.46391,0.46353,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-02-11,Multi-stage,Embryo,Whole Organism,All anatomical structures
68544,SRR17994491,SRX14150131,SRS11975601,SRP359470,PRJNA806206,RNA seq for psip1a knockdown,PRJNA806206,Other,Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them  Psip1  the gene codes LEDGF/p75  has been implicated in cancer  autoimmune diseases and HIV pathogenesis. However  the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.,,,,,psip1aMO 1,,strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish embryos psip1a MO,psip1a MO1,psip1a MO1,The cDNA Library construction and quality control were coordinated by Novogen co.  Ltd,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP359470,,assembly:GRCz10,PSIP1AMO_experiment1_sorted.bam,bam,6695117700.0,22317059.0,PSIP1AMO experiment1 sorted.bam,0:150 1:150,A:1786397578;C:1577152264;G:1568675842;T:1762687628;N:204388,150,150,,,1786397578,1577152264,1568675842,1762687628,204388,SRX14150131,SRS11975601,SRA1370574,UC Merced|Bioengineering,UC Merced,2,0.95203,0.95199,0.07618,0.07659,0.6845,0.68495,0.46729,0.46789,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-02-11,Multi-stage,Embryo,Whole Organism,All anatomical structures