metadata: run_metadata: 75 rows where experiment.library_selection = "RT-PCR" and tissue

75 rows where experiment.library_selection = "RT-PCR" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30599	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	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	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	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	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	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	30716	SRR28342048	SRX23948605	SRS20750294	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag RESA CLIP input B3	3xflag RESA CLIP input B3 AGN003279	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002510\|replicate ref:AGN003279\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 input\|replicate label short:RESA CLIP Upf1 #3737 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B3	AGR004059	AGR004059	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004059_R1.fastq AGR004059_R2.fastq	fastq fastq	15446715026.0	51148063.0	AGR004059 R1.fastq.zst	0:151 1:151	A:4298384942;C:3080575022;G:4004069877;T:4063619821;N:65364	151	151	4298384942	3080575022	4004069877	4063619821	65364	SRX23948605	SRS20750294	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30717	30717	SRR28342039	SRX23948614	SRS20750302	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 R843C RESA HITS CLIP B1	3xflag upf1 R843C RESA HITS CLIP B1 AGN003273	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002507\|replicate ref:AGN003273\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 IP\|replicate label short:RESA CLIP Upf1 #3735 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 R843C RESA HITS CLIP B1	AGR004053	AGR004053	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004053_R1.fastq AGR004053_R2.fastq	fastq fastq	10545264992.0	34918096.0	AGR004053 R1.fastq.zst	0:151 1:151	A:2943441620;C:2155828506;G:2709854276;T:2736095568;N:45022	151	151	2943441620	2155828506	2709854276	2736095568	45022	SRX23948614	SRS20750302	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30718	30718	SRR28342040	SRX23948613	SRS20750303	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 C126S RESA HITS CLIP B2	3xflag upf1 C126S RESA HITS CLIP B2 AGN003282	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002511\|replicate ref:AGN003282\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 IP\|replicate label short:RESA CLIP Upf1 #3737 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 C126S RESA HITS CLIP B2	AGR004062	AGR004062	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004062_R1.fastq AGR004062_R2.fastq	fastq fastq	11134300590.0	36868545.0	AGR004062 R1.fastq.zst	0:151 1:151	A:3063023630;C:2386509106;G:2925940275;T:2758782993;N:44586	151	151	3063023630	2386509106	2925940275	2758782993	44586	SRX23948613	SRS20750303	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30719	30719	SRR28342041	SRX23948612	SRS20750301	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 C126S RESA HITS CLIP B1	3xflag upf1 C126S RESA HITS CLIP B1 AGN003281	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002511\|replicate ref:AGN003281\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3737 IP\|replicate label short:RESA CLIP Upf1 #3737 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 C126S RESA HITS CLIP B1	AGR004061	AGR004061	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004061_R1.fastq AGR004061_R2.fastq	fastq fastq	13368435586.0	44266343.0	AGR004061 R1.fastq.zst	0:151 1:151	A:3603822055;C:2659540495;G:3591989409;T:3513026539;N:57088	151	151	3603822055	2659540495	3591989409	3513026539	57088	SRX23948612	SRS20750301	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30720	30720	SRR28342042	SRX23948611	SRS20750300	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 G495R/G497E RESA HITS CLIP B2	3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGN003278	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002509\|replicate ref:AGN003278\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 IP\|replicate label short:RESA CLIP Upf1 #3736 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 G495R/G497E RESA HITS CLIP B2	AGR004058	AGR004058	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004058_R1.fastq AGR004058_R2.fastq	fastq fastq	13750586084.0	45531742.0	AGR004058 R1.fastq.zst	0:151 1:151	A:3775460380;C:2748834924;G:3672092546;T:3554141983;N:56251	151	151	3775460380	2748834924	3672092546	3554141983	56251	SRX23948611	SRS20750300	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30721	30721	SRR28342043	SRX23948610	SRS20750299	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 G495R/G497E RESA HITS CLIP B1	3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGN003277	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002509\|replicate ref:AGN003277\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 IP\|replicate label short:RESA CLIP Upf1 #3736 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 G495R/G497E RESA HITS CLIP B1	AGR004057	AGR004057	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004057_R1.fastq AGR004057_R2.fastq	fastq fastq	10708529212.0	35458706.0	AGR004057 R1.fastq.zst	0:151 1:151	A:2983511099;C:2231542625;G:2842811089;T:2650619142;N:45257	151	151	2983511099	2231542625	2842811089	2650619142	45257	SRX23948610	SRS20750299	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30722	30722	SRR28342044	SRX23948609	SRS20750297	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag gfp RESA HITS CLIP B1	3xflag gfp RESA HITS CLIP B1 AGN002579	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 01 05\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS001970\|replicate ref:AGN002579\|replicate order:1\|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:gfp CLIP\|replicate label short:gfp CLIP B1\|BioSampleModel:Model organism or animal	3xflag gfp RESA HITS CLIP B1	AGR003308	AGR003308	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003308_R1.fastq AGR003308_R2.fastq	fastq fastq	507167460.0	2510730.0	AGR003308 R1.fastq.zst	0:101 1:101	A:156207937;C:97169427;G:111291367;T:142479104;N:19625	101	101	156207937	97169427	111291367	142479104	19625	SRX23948609	SRS20750297	SRA1824033	Yale University\|Genetics	Yale University												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30723	30723	SRR28342045	SRX23948608	SRS20750298	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag RESA HITS CLIP input B4	3xflag RESA CLIP input B4 AGN003267	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002504\|replicate ref:AGN003267\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 input\|replicate label short:RESA CLIP Upf1 #3650 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B4	AGR004047	AGR004047	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004047_R2.fastq AGR004047_R1.fastq	fastq fastq	19396379142.0	64226421.0	AGR004047 R1.fastq.zst	0:151 1:151	A:5606633601;C:3872715770;G:4910603410;T:5006345083;N:81278	151	151	5606633601	3872715770	4910603410	5006345083	81278	SRX23948608	SRS20750298	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30724	30724	SRR28342046	SRX23948607	SRS20750295	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf3b RESA HITS CLIP B2	3xflag upf3b RESA HITS CLIP B2 AGN002796	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002161\|replicate ref:AGN002796\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3b pulldown\|replicate label short:Upf3b pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf3b RESA HITS CLIP B2	AGR003554	AGR003554	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003554_R1.fastq AGR003554_R2.fastq	fastq fastq	9047261244.0	44788422.0	AGR003554 R1.fastq.zst	0:101 1:101	A:2711585737;C:1825740983;G:2076537283;T:2433050799;N:346442	101	101	2711585737	1825740983	2076537283	2433050799	346442	SRX23948607	SRS20750295	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30725	30725	SRR28342047	SRX23948606	SRS20750296	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf3b RESA HITS CLIP B1	3xflag upf3b RESA HITS CLIP B1 AGN002795	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002161\|replicate ref:AGN002795\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3b pulldown\|replicate label short:Upf3b pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf3b RESA HITS CLIP B1	AGR003549	AGR003549	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003549_R1.fastq AGR003549_R2.fastq	fastq fastq	9617196770.0	47609885.0	AGR003549 R1.fastq.zst	0:101 1:101	A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990	101	101	2856263963	1963091501	2218118010	2579364306	358990	SRX23948606	SRS20750296	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30726	30726	SRR28342049	SRX23948604	SRS20750292	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf3a RESA HITS CLIP B2	3xflag upf3a RESA HITS CLIP B2 AGN002792	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002159\|replicate ref:AGN002792\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3a pulldown\|replicate label short:Upf3a pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf3a RESA HITS CLIP B2	AGR003566	AGR003566	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003566_R1.fastq AGR003566_R2.fastq	fastq fastq	50318544410.0	249101705.0	AGR003566 R1.fastq.zst	0:101 1:101	A:14930547705;C:10295739682;G:11624332741;T:13466693890;N:1230392	101	101	14930547705	10295739682	11624332741	13466693890	1230392	SRX23948604	SRS20750292	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30727	30727	SRR28342050	SRX23948603	SRS20750293	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf3a RESA HITS CLIP B1	3xflag upf3a RESA HITS CLIP B1 AGN002791	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002159\|replicate ref:AGN002791\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf3a pulldown\|replicate label short:Upf3a pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf3a RESA HITS CLIP B1	AGR003545	AGR003545	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003545_R1.fastq AGR003545_R2.fastq	fastq fastq	10770959564.0	53321582.0	AGR003545 R1.fastq.zst	0:101 1:101	A:3207646854;C:2186852059;G:2481889724;T:2894165865;N:405062	101	101	3207646854	2186852059	2481889724	2894165865	405062	SRX23948603	SRS20750293	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30728	30728	SRR28342051	SRX23948602	SRS20750291	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf2 RESA HITS CLIP B2	3xflag upf2 RESA HITS CLIP B2 AGN002788	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002157\|replicate ref:AGN002788\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf2 pulldown\|replicate label short:Upf2 pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf2 RESA HITS CLIP B2	AGR003541	AGR003541	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003541_R1.fastq AGR003541_R2.fastq	fastq fastq	9471117440.0	46886720.0	AGR003541 R1.fastq.zst	0:101 1:101	A:2852420143;C:1898246719;G:2136843599;T:2583254674;N:352305	101	101	2852420143	1898246719	2136843599	2583254674	352305	SRX23948602	SRS20750291	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30729	30729	SRR28342052	SRX23948601	SRS20750290	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf2 RESA HITS CLIP B1	3xflag upf2 RESA HITS CLIP B1 AGN002787	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002157\|replicate ref:AGN002787\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf2 pulldown\|replicate label short:Upf2 pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf2 RESA HITS CLIP B1	AGR003542	AGR003542	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003542_R1.fastq AGR003542_R2.fastq	fastq fastq	10845546044.0	53690822.0	AGR003542 R1.fastq.zst	0:101 1:101	A:3277705832;C:2154122837;G:2449408891;T:2963913264;N:395220	101	101	3277705832	2154122837	2449408891	2963913264	395220	SRX23948601	SRS20750290	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30730	30730	SRR28342053	SRX23948600	SRS20750289	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 RESA HITS CLIP B5	3xflag upf1 RESA HITS CLIP B5 AGN003270	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002505\|replicate ref:AGN003270\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 IP\|replicate label short:RESA CLIP Upf1 #3650 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B5	AGR004050	AGR004050	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004050_R1.fastq AGR004050_R2.fastq	fastq fastq	11823214534.0	39149717.0	AGR004050 R1.fastq.zst	0:151 1:151	A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480	151	151	3184473505	2558650081	3236214151	2843828317	48480	SRX23948600	SRS20750289	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30731	30731	SRR28342054	SRX23948599	SRS20750288	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 RESA HITS CLIP B4	3xflag upf1 RESA HITS CLIP B4 AGN003269	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002505\|replicate ref:AGN003269\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3650 IP\|replicate label short:RESA CLIP Upf1 #3650 IP B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B4	AGR004049	AGR004049	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004049_R1.fastq AGR004049_R2.fastq	fastq fastq	14371221754.0	47586827.0	AGR004049 R1.fastq.zst	0:151 1:151	A:3983698498;C:2912453835;G:3805806498;T:3669203887;N:59036	151	151	3983698498	2912453835	3805806498	3669203887	59036	SRX23948599	SRS20750288	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30732	30732	SRR28342055	SRX23948598	SRS20750287	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 RESA HITS CLIP B3	3xflag upf1 RESA HITS CLIP B3 AGN002798	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002154\|replicate ref:AGN002798\|replicate order:2\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf1 pulldown\|replicate label short:Upf1 pulldown B2\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B3	AGR003555	AGR003555	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003555_R1.fastq AGR003555_R2.fastq	fastq fastq	13605076932.0	67351866.0	AGR003555 R1.fastq.zst	0:101 1:101	A:3996372048;C:2823464384;G:3156030119;T:3628752419;N:457962	101	101	3996372048	2823464384	3156030119	3628752419	457962	SRX23948598	SRS20750287	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30733	30733	SRR28342056	SRX23948597	SRS20750283	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 RESA HITS CLIP B2	3xflag upf1 RESA HITS CLIP B2 AGN002784	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 08 19\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002154\|replicate ref:AGN002784\|replicate order:1\|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:Upf1 pulldown\|replicate label short:Upf1 pulldown B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B2	AGR003552	AGR003552	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003552_R1.fastq AGR003552_R2.fastq	fastq fastq	10762870878.0	53281539.0	AGR003552 R1.fastq.zst	0:101 1:101	A:3170047840;C:2223795927;G:2504911576;T:2863700088;N:415447	101	101	3170047840	2223795927	2504911576	2863700088	415447	SRX23948597	SRS20750283	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30734	30734	SRR28342057	SRX23948596	SRS20750286	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 RESA HITS CLIP B1	3xflag upf1 RESA HITS CLIP B1 AGN002577	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2021 01 05\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS001968\|replicate ref:AGN002577\|replicate order:1\|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp\|project label short:3xflag upf1 RESA HITS CLIP\|sample label short:upf1 CLIP\|replicate label short:upf1 CLIP B1\|BioSampleModel:Model organism or animal	3xflag upf1 RESA HITS CLIP B1	AGR003306	AGR003306	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR003306_R1.fastq AGR003306_R2.fastq	fastq fastq	529433718.0	2620959.0	AGR003306 R1.fastq.zst	0:101 1:101	A:157881697;C:106579975;G:122214915;T:142736640;N:20491	101	101	157881697	106579975	122214915	142736640	20491	SRX23948596	SRS20750286	SRA1824033	Yale University\|Genetics	Yale University												B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30735	30735	SRR28342058	SRX23948595	SRS20750284	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag upf1 R843C RESA HITS CLIP B2	3xflag upf1 R843C RESA HITS CLIP B2 AGN003274	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002507\|replicate ref:AGN003274\|replicate order:2\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 IP\|replicate label short:RESA CLIP Upf1 #3735 IP B2\|BioSampleModel:Model organism or animal	3xflag upf1 R843C RESA HITS CLIP B2	AGR004054	AGR004054	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004054_R1.fastq AGR004054_R2.fastq	fastq fastq	12067359790.0	39958145.0	AGR004054 R1.fastq.zst	0:151 1:151	A:3301899297;C:2532414363;G:3161463027;T:3071532640;N:50463	151	151	3301899297	2532414363	3161463027	3071532640	50463	SRX23948595	SRS20750284	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30736	30736	SRR28342059	SRX23948594	SRS20750282	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag RESA CLIP input B2	3xflag RESA CLIP input B2 AGN003275	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002508\|replicate ref:AGN003275\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3736 input\|replicate label short:RESA CLIP Upf1 #3736 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B2	AGR004055	AGR004055	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004055_R1.fastq AGR004055_R2.fastq	fastq fastq	13295917534.0	44026217.0	AGR004055 R1.fastq.zst	0:151 1:151	A:3866188367;C:2751508227;G:3344357660;T:3333805406;N:57874	151	151	3866188367	2751508227	3344357660	3333805406	57874	SRX23948594	SRS20750282	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
30737	30737	SRR28342060	SRX23948593	SRS20750285	SRP495203	PRJNA1087701	UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP.	PRJNA1087701	Other	Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.			3xflag RESA CLIP input B1	3xflag RESA CLIP input B1 AGN003271	strain:TU/AB\|age:3.5 hpf\|dev stage:1k cell\|collection date:2022 10 04\|geo loc name:USA\|sex:pooled male and female\|tissue:embryo\|genotype:wt\|strain maternal:wt\|strain paternal:wt\|molecule:mRNA\|selection:flag bead PD post crosslinking\|sample ref:AGS002506\|replicate ref:AGN003271\|replicate order:1\|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper\|project label short:upf1 mutant RESA HITS CLIP\|sample label short:RESA CLIP Upf1 #3735 input\|replicate label short:RESA CLIP Upf1 #3735 input B1\|BioSampleModel:Model organism or animal	3xflag RESA HITS CLIP input B1	AGR004051	AGR004051	PCR from library specific RT	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495203	AGR004051_R1.fastq AGR004051_R2.fastq	fastq fastq	14891006336.0	49307968.0	AGR004051 R1.fastq.zst	0:151 1:151	A:4241333172;C:3027167277;G:3764089225;T:3858355544;N:61118	151	151	4241333172	3027167277	3764089225	3858355544	61118	SRX23948593	SRS20750285	SRA1824033	Yale University\|Genetics	Yale University												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2024-03-14	Blastula	Embryo	Embryo Imprecise	All anatomical structures
33326	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	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	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	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	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	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
43660	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	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	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
55296	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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
62799	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	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	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	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	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	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	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	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	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	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	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	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
71388	71388	SRR21528734	SRX17531094	SRS15079603	SRP396673	PRJNA879284	Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos	PRJNA879284	Other				HCQ embryos	HCQ embryos	strain:AB\|breed:Egg water\|age:0.8year\|dev stage:5hpf\|sex:not applicable\|tissue:embryo\|cell line:embryo\|cell type:embryo\|collected by:Straw\|BioSampleModel:Model organism or animal	RNA Seq of HCQ embryo	2	2	HCQ embryo	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP396673	HCQ_1.fq.gz HCQ_2.fq.gz	fastq fastq	6247416600.0	20824722.0	HCQ 1.fq.gz	0:150 1:150	A:1705532494;C:1419469418;G:1445959454;T:1676101471;N:353763	150	150	1705532494	1419469418	1445959454	1676101471	353763	SRX17531094	SRS15079603	SRA1495070	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.95531	0.95352	0.05755	0.05707	0.7513	0.75215	0.48749	0.48711	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2022-09-12	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
71389	71389	SRR21528735	SRX17531093	SRS15079603	SRP396673	PRJNA879284	Toxicology evaluation of overdose hydroxychloroquine on zebrafish Danio rerio embryos	PRJNA879284	Other				HCQ embryos	HCQ embryos	strain:AB\|breed:Egg water\|age:0.8year\|dev stage:5hpf\|sex:not applicable\|tissue:embryo\|cell line:embryo\|cell type:embryo\|collected by:Straw\|BioSampleModel:Model organism or animal	RNA Seq of WT embryo	1	1	WT embryo	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP396673	HCQ-con_1.fq.gz HCQ-con_2.fq.gz	fastq fastq	6039833100.0	20132777.0	HCQ con 1.fq.gz	0:150 1:150	A:1632793916;C:1383182551;G:1413411225;T:1610087974;N:357434	150	150	1632793916	1383182551	1413411225	1610087974	357434	SRX17531093	SRS15079603	SRA1495070	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.95216	0.95061	0.05402	0.05357	0.75185	0.75262	0.48712	0.48749	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2022-09-12	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
75644	75644	SRR24752590	SRX20528694	SRS17837826	SRP439887	PRJNA976915	Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976915	Other	Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			Embryos 5hpf	Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal	RNA Seq of Embryo 5hpf Gentanicin	2	2	Embryo 5hpf Gentanicin	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP439887	Qingda_1.fq.gz Qingda_2.fq.gz	fastq fastq	6985244400.0	23284148.0	Qingda 1.fq.gz	0:150 1:150	A:1634658220;C:1842974934;G:1881072995;T:1626517291;N:20960	150	150	1634658220	1842974934	1881072995	1626517291	20960	SRX20528694	SRS17837826	SRA1645398	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.96818	0.97235	0.21368	0.21914	0.79265	0.79273	0.53525	0.50366	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures
75645	75645	SRR24752591	SRX20528693	SRS17837826	SRP439887	PRJNA976915	Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976915	Other	Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			Embryos 5hpf	Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal	RNA Seq of WT Embryo 5hpf	1	1	WT Embryo 5hpf	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP439887	WT-blank_1.fq.gz WT-blank_2.fq.gz	fastq fastq	6062337300.0	20207791.0	WT blank 1.fq.gz	0:150 1:150	A:1526499059;C:1498285888;G:1526586728;T:1510947161;N:18464	150	150	1526499059	1498285888	1526586728	1510947161	18464	SRX20528693	SRS17837826	SRA1645398	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.96896	0.97182	0.02595	0.02539	0.77861	0.77865	0.48078	0.48377	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures
75646	75646	SRR24754508	SRX20530612	SRS17839502	SRP439912	PRJNA976946	MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976946	Other	MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			m6A Embryos 5hpf	m6A Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal	MeRIP Seq of Embryo 5hpf Gentanicin	2	2	Embryo 5hpf Gentanicin	RIP-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP439912	QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz	fastq fastq fastq fastq	16015155900.0	53383853.0	QingdaIP 1.fq.gz	0:150 1:150	A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972	150	150	3341079522	3427050846	6045646273	3201293287	85972	SRX20530612	SRS17839502	SRA1645459	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.75159	0.73659	0.1359	0.13542	0.8117	0.81172	0.51543	0.51251	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures
75647	75647	SRR24754509	SRX20530611	SRS17839502	SRP439912	PRJNA976946	MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model	PRJNA976946	Other	MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model			m6A Embryos 5hpf	m6A Embryos 5hpf	strain:AB\|breed:Egg water\|age:5hpf\|dev stage:5hpf\|sex:not applicable\|tissue:Embryos\|BioSampleModel:Model organism or animal	MeRIP Seq of WT Embryo 5hpf	1	1	WT Embryo 5hpf	RIP-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP439912	WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz	fastq fastq fastq fastq	15326922600.0	51089742.0	WT blankIP 1.fq.gz	0:150 1:150	A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844	150	150	3289509867	3239692571	5510216977	3287142341	360844	SRX20530611	SRS17839502	SRA1645459	Sichuan University\|West China Second University Hospital	Sichuan University	2	0.71182	0.69789	0.02169	0.02058	0.80409	0.80395	0.47813	0.48125	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2023-05-27	Blastula	Embryo	Embryo Imprecise	All anatomical structures
77327	77327	SRR065197	SRX026483	SRS114570	SRP003472	PRJXX3472	RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation	ZF_U1C	Transcriptome Analysis	Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.	pubmed:21468032	Total RNA from 3 dpf mutant zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library.	Total RNA from 3 dpf mutant zebrafish embryos	MUT		3 dpf mutant zebrafish embryos	MUT	mut	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>	SRP003472	MUT_1.txt.tar.gz MUT_2N.txt.tar.gz MUT_3.txt.tar.gz	fastq fastq fastq	2418427464.0	31821414.0	MUT	0:76	A:604956506;C:600954722;G:608767958;T:600808464;N:2939814	76		604956506	600954722	608767958	600808464	2939814	SRX026483	SRS114570			Justus-Liebig University Giessen	1	0.91109		0.077		0.71445		0.44387		76		B		usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	unknown	unknown	Germany	2011-03-31	Larval	Larval	Embryo Imprecise	All anatomical structures
77328	77328	SRR065196	SRX026482	SRS114569	SRP003472	PRJXX3472	RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation	ZF_U1C	Transcriptome Analysis	Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.	pubmed:21468032	Total RNA from 3 dpf wildtype zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library.	Total RNA from 3 dpf wildtype zebrafish embryos	WT		3 dpf wildtype embryos	WT	wt	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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>	SRP003472	WT_1.txt.tar WT_2.txt.tar.gz WT_3.txt.tar.gz WT_4.txt.tar.gz	fastq fastq fastq fastq	2697785376.0	35497176.0	WT	0:76	A:676186765;C:669131645;G:670872323;T:676745206;N:4849437	76		676186765	669131645	670872323	676745206	4849437	SRX026482	SRS114569			Justus-Liebig University Giessen	1	0.9435		0.087		0.71429		0.46075		76		B		usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	unknown	unknown	Germany	2011-03-31	Larval	Larval	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;