metadata: run_metadata: 38 rows where devstage_curation_coarse = "Juvenile" and experiment.library

38 rows where devstage_curation_coarse = "Juvenile" and experiment.library_selection = "RT-PCR"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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.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
34128	34128	SRR31371655	SRX26745254	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PC3 R1.fq	PC3 R1.fq	CuNPs and melatonin treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PC3_R1.fq.gz PC3_R2.fq.gz	fastq fastq	8050557450.0	26657475.0	PC3 R1.fq.gz										SRX26745254	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34129	34129	SRR31371656	SRX26745253	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PC2 R1.fq	PC2 R1.fq	CuNPs and melatonin treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PC2_R1.fq.gz PC2_R2.fq.gz	fastq fastq	7072903722.0	23420211.0	PC2 R1.fq.gz	0:151 1:151	A:1848366962;C:1685927772;G:1702568524;T:1835518466;N:521998	151	151	1848366962	1685927772	1702568524	1835518466	521998	SRX26745253	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34130	34130	SRR31371657	SRX26745252	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PC1 R1.fq	PC1 R1.fq	CuNPs and melatonin treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PC1_R1.fq.gz PC1_R2.fq.gz	fastq fastq	9551575668.0	31627734.0	PC1 R1.fq.gz										SRX26745252	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34131	34131	SRR31371658	SRX26745251	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PB3 R1.fq	PB3 R1.fq	CuNPs treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PB3_R1.fq.gz PB3_R2.fq.gz	fastq fastq	6839092000.0	22646000.0	PB3 R1.fq.gz										SRX26745251	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34132	34132	SRR31371659	SRX26745250	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PB2 R1.fq	PB2 R1.fq	CuNPs treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PB2_R1.fq.gz PB2_R2.fq.gz	fastq fastq	7582292558.0	25106929.0	PB2 R1.fq.gz										SRX26745250	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34133	34133	SRR31371660	SRX26745249	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	PB1 R1.fq	PB1 R1.fq	CuNPs treatment	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	PB1_R1.fq.gz PB1_R2.fq.gz	fastq fastq	8122972218.0	26897259.0	PB1 R1.fq.gz										SRX26745249	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34134	34134	SRR31371661	SRX26745248	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	CA3 R1.fq	CA3 R1.fq	control	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	CA3_R1.fq.gz CA3_R2.fq.gz	fastq fastq	7638136586.0	25291843.0	CA3 R1.fq.gz										SRX26745248	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34135	34135	SRR31371662	SRX26745247	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	CA1 R1.fq	CA1 R1.fq	control	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	CA1_R1.fq.gz CA1_R2.fq.gz	fastq fastq	7499744784.0	24833592.0	CA1 R1.fq.gz	0:151 1:151	A:1951636355;C:1801626786;G:1812560367;T:1933366696;N:554580	151	151	1951636355	1801626786	1812560367	1933366696	554580	SRX26745247	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
34136	34136	SRR31371663	SRX26745246	SRS23234144	SRP545712	PRJNA1186363	Danio rerio Transcriptome or Gene expression	PRJNA1186363	Other	Gonad tissue of juvenile zebrafish post long term treatment with nano copper or melatonin		Model organism or animal sample from zebrafish	zebra001	cultivar:zebrafish\|age:40dpf\|collection date:2024 11 15\|geo loc name:China\|sex:female\|tissue:Freshwater Fisheries Research Center of ChineseAcademy of Fishery Sciences\|zebrafish:Gonadal development\|BioSampleModel:Model organism or animal	RNA seq from the gonad of Zebrafish	CA2 R1.fq	CA2 R1.fq	control	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina NovaSeq X Plus	SRP545712	CA2_R1.fq.gz CA2_R2.fq.gz	fastq fastq	6253035330.0	20705415.0	CA2 R1.fq.gz										SRX26745246	SRS23234144	SRA2016483	Chinese Academy of Fishery Science\|Freshwater Fishery Research Center	Chinese Academy of Fishery Science												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-11-17	Juvenile	Juvenile	Gonad	Reproductive System
42181	42181	SRR5482153	SRX2765568	SRS2149771	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 1 F2 offspring originating from wild caught population	LS1 F2	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2008\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals	LS1 F2	LS1 F2	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS1-F2-10_FCC4CMHACXX_L1_WHZEBagiNCADRAAPEI-205_1.fq.gz LS1-F2-1_FCC4BKHACXX_L7_WHZEBagiNCAARAAPEI-201_1.fq.gz LS1-F2-5_FCC4BKHACXX_L7_WHZEBagiNCABRAAPEI-202_1.fq.gz LS1-F2-8_FCC4BKHACXX_L7_WHZEBagiNCACRAAPEI-203_1.fq.gz	fastq fastq fastq fastq	12496905120.0	255038880.0	LS1 F2 10 FCC4CMHACXX L1 WHZEBagiNCADRAAPEI 205 1.fq.gz	0:49	A:3275093505;C:2981786839;G:2904373605;T:3334855308;N:795863	49		3275093505	2981786839	2904373605	3334855308	795863	SRX2765568	SRS2149771	SRA557107	University of Turku\|Biology	University of Turku	1	0.88577		0.04599		0.76469		0.48703		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42182	42182	SRR5482152	SRX2765567	SRS2149770	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 2 F2 offspring originating from wild caught population	LS2 F2	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2008\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals	LS2 F2	LS2 F2	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS2-F2-10_FCC4CMHACXX_L4_WHZEBagiNCALRAAPEI-213_1.fq.gz LS2-F2-11_FCC4CMHACXX_L4_WHZEBagiNCAMRAAPEI-214_1.fq.gz LS2-F2-14_FCC4C2AACXX_L1_WHZEBagiNCANRAAPEI-215_1.fq.gz LS2-F2-9_FCC4CMHACXX_L4_WHZEBagiNCAKRAAPEI-212_1.fq.gz	fastq fastq fastq fastq	11108547205.0	226705045.0	LS2 F2 9 FCC4CMHACXX L4 WHZEBagiNCAKRAAPEI 212 1.fq.gz	0:49	A:2930693084;C:2628276474;G:2564131315;T:2984423047;N:1023285	49		2930693084	2628276474	2564131315	2984423047	1023285	SRX2765567	SRS2149770	SRA557107	University of Turku\|Biology	University of Turku	1	0.90013		0.04677		0.81251		0.44762		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42183	42183	SRR5482151	SRX2765565	SRS2149769	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 1 F2 offspring originating from wild caught population	RS1 F2	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2008\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals	RS1 F2	RS1 F2	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS1-F2-14_FCC4C2AACXX_L2_WHZEBagiNCAURAAPEI-223_1.fq.gz RS1-F2-16_FCC4C2AACXX_L2_WHZEBagiNCAVRAAPEI-225_1.fq.gz RS1-F2-17_FCC4C2AACXX_L3_WHZEBagiNCAWRAAPEI-227_1.fq.gz RS1-F2-19_FCC4C2AACXX_L3_WHZEBagiNCAXRAAPEI-201_1.fq.gz	fastq fastq fastq fastq	12074501894.0	246418406.0	RS1 F2 16 FCC4C2AACXX L2 WHZEBagiNCAVRAAPEI 225 1.fq.gz	0:49	A:3199737416;C:2851335695;G:2767557430;T:3254746975;N:1124378	49		3199737416	2851335695	2767557430	3254746975	1124378	SRX2765565	SRS2149769	SRA557107	University of Turku\|Biology	University of Turku	1	0.87838		0.05071		0.81663		0.55417		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42184	42184	SRR5482150	SRX2765564	SRS2149768	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 2 F2 offspring originating from wild caught population	RS2 F2	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2008\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F2 individuals	RS2 F2	RS2 F2	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS2-F2-3_FCC4CMHACXX_L2_WHZEBagiNCBFRAAPEI-210_1.fq.gz RS2-F2-6-2_FCC4CMHACXX_L2_WHZEBagiNCBGRAAPEI-211_1.fq.gz RS2-F2-8_FCC4CMHACXX_L2_WHZEBagiNCBHRABPEI-212_1.fq.gz RS2-F2-9_FCC4CMHACXX_L3_WHZEBagiNCBIRABPEI-213_1.fq.gz	fastq fastq fastq fastq	11923597525.0	243338725.0	RS2 F2 9 FCC4CMHACXX L3 WHZEBagiNCBIRABPEI 213 1.fq.gz	0:49	A:3132507165;C:2819390547;G:2776793842;T:3193588286;N:1317685	49		3132507165	2819390547	2776793842	3193588286	1317685	SRX2765564	SRS2149768	SRA557107	University of Turku\|Biology	University of Turku	1	0.90986		0.05269		0.814		0.36827		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42185	42185	SRR5482149	SRX2765563	SRS2149767	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 1 F5 offspring originating from wild caught population	LS1 F5	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2010\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals	LS1 F5	LS1 F5	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS1-15_FCC4C3HACXX_L1_WHZEBagiNBANRAAPEI-215_1.fq.gz LS1-2_FCC4BJ2ACXX_L5_WHZEBagiNBABRAAPEI-202_1.fq.gz LS1-6_FCC4BJ2ACXX_L6_WHZEBagiNBAFRAAPEI-207_1.fq.gz LS1-8_FCC4BJ2ACXX_L8_WHZEBagiNBAJRAAPEI-211_1.fq.gz	fastq fastq fastq fastq	12776192331.0	260738619.0	LS1 2 FCC4BJ2ACXX L5 WHZEBagiNBABRAAPEI 202 1.fq.gz	0:49	A:3371838433;C:3025006624;G:2934135898;T:3444117388;N:1093988	49		3371838433	3025006624	2934135898	3444117388	1093988	SRX2765563	SRS2149767	SRA557107	University of Turku\|Biology	University of Turku	1	0.88482		0.04932		0.813		0.51224		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42186	42186	SRR5482148	SRX2765562	SRS2149766	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 2 F5 offspring originating from wild caught population	LS2 F5	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2010\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals	LS2 F5	LS2 F5	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS2-10_FCC4BJ2ACXX_L8_WHZEBagiNBAKRAAPEI-212_1.fq.gz LS2-11_FCC4C3HACXX_L1_WHZEBagiNBAORAAPEI-216_1.fq.gz LS2-1_FCC4BJ2ACXX_L5_WHZEBagiNBACRAAPEI-203_1.fq.gz LS2-7_FCC4BVYACXX_L1_WHZEBagiNBAGRAAPEI-208_1.fq.gz	fastq fastq fastq fastq	11941143935.0	243696815.0	LS2 10 FCC4BJ2ACXX L8 WHZEBagiNBAKRAAPEI 212 1.fq.gz	0:49	A:3165540142;C:2817777586;G:2733117846;T:3223679054;N:1029307	49		3165540142	2817777586	2733117846	3223679054	1029307	SRX2765562	SRS2149766	SRA557107	University of Turku\|Biology	University of Turku	1	0.87119		0.04752		0.80251		0.55444		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42187	42187	SRR5482147	SRX2765561	SRS2149765	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 1 F5 offspring originating from wild caught population	RS1 F5	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2010\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals	RS1 F5	RS1 F5	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS1-10_FCC4BJ2ACXX_L8_WHZEBagiNBALRAAPEI-213_1.fq.gz RS1-2_FCC4Y2GACXX_L4_WHZEBagiNCBPRABPEI-221_1.fq.gz RS1-3_FCC4BJ2ACXX_L6_WHZEBagiNBADRAAPEI-205_1.fq.gz RS1-6_FCC4BV7ACXX_L1_WHZEBagiNBAHRAAPEI-209_1.fq.gz	fastq fastq fastq fastq	12149652753.0	247952097.0	RS1 6 FCC4BV7ACXX L1 WHZEBagiNBAHRAAPEI 209 1.fq.gz	0:49	A:3177681868;C:2907323525;G:2822484622;T:3241144133;N:1018605	49		3177681868	2907323525	2822484622	3241144133	1018605	SRX2765561	SRS2149765	SRA557107	University of Turku\|Biology	University of Turku	1	0.90495		0.04625		0.80028		0.56443		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42188	42188	SRR5482146	SRX2765560	SRS2149764	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 2 F5 offspring originating from wild caught population	RS2 F5	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2010\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F5 individuals	RS2 F5	RS2 F5	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS2-10_FCC4BVYACXX_L1_WHZEBagiNBAIRAAPEI-210_1.fq.gz RS2-13_FCC4C3HACXX_L1_WHZEBagiNBAMRAAPEI-214_1.fq.gz RS2-2_FCC4BJ2ACXX_L5_WHZEBagiNBAARAAPEI-201_1.fq.gz RS2-3_FCC4C19ACXX_L5_WHZEBagiNBAERAAPEI-206_1.fq.gz	fastq fastq fastq fastq	11262796951.0	229852999.0	RS2 13 FCC4C3HACXX L1 WHZEBagiNBAMRAAPEI 214 1.fq.gz	0:49	A:2931626627;C:2710523895;G:2627211912;T:2992545637;N:888880	49		2931626627	2710523895	2627211912	2992545637	888880	SRX2765560	SRS2149764	SRA557107	University of Turku\|Biology	University of Turku	1	0.88588		0.04266		0.8112		0.52927		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42189	42189	SRR5482145	SRX2765559	SRS2149763	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 1 F11 offspring originating from wild caught population	LS1 F11	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2014\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals	LS1 F11	LS1 F11	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS1-F11B-11_FCC4CMHACXX_L1_WHZEBagiNCAERAAPEI-206_1.fq.gz LS1-F11B-13_FCC4CMHACXX_L1_WHZEBagiNCAFRAAPEI-207_1.fq.gz LS1-F11B-16_FCC4C19ACXX_L1_WHZEBagiNCAGRBAPEI-208_1.fq.gz LS1-F11B-17_FCC4BKHACXX_L8_WHZEBagiNCAHRAAPEI-209_1.fq.gz	fastq fastq fastq fastq	11326213584.0	231147216.0	LS1 F11B 16 FCC4C19ACXX L1 WHZEBagiNCAGRBAPEI 208 1.fq.gz	0:49	A:2982223592;C:2693407623;G:2622876703;T:3026833843;N:871823	49		2982223592	2693407623	2622876703	3026833843	871823	SRX2765559	SRS2149763	SRA557107	University of Turku\|Biology	University of Turku	1	0.90202		0.04273		0.78273		0.51238		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42190	42190	SRR5482144	SRX2765558	SRS2149762	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Large harvested line biological replicate 2 F11 offspring originating from wild caught population	LS2 F11	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2014\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F11 individuals	LS2 F11	LS2 F11	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	LS2-F11B-1_FCC4C2AACXX_L1_WHZEBagiNCAORAAPEI-216_1.fq.gz LS2-F11B-2_FCC4C2AACXX_L1_WHZEBagiNCAPRAAPEI-218_1.fq.gz LS2-F11B-5_FCC4CMHACXX_L5_WHZEBagiNCAQRAAPEI-219_1.fq.gz LS2-F11B-7_FCC4CMHACXX_L5_WHZEBagiNCARRAAPEI-220_1.fq.gz	fastq fastq fastq fastq	12030571875.0	245521875.0	LS2 F11B 7 FCC4CMHACXX L5 WHZEBagiNCARRAAPEI 220 1.fq.gz	0:49	A:3149792862;C:2871072895;G:2795019949;T:3213514581;N:1171588	49		3149792862	2871072895	2795019949	3213514581	1171588	SRX2765558	SRS2149762	SRA557107	University of Turku\|Biology	University of Turku	1	0.91893		0.036		0.77429		0.38962		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42191	42191	SRR5482143	SRX2765557	SRS2149760	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 1 F11 offspring originating from wild caught population	RS1 F11	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2014\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals	RS1 F11	RS1 F11	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS1-F11B-21_FCC4C2AACXX_L3_WHZEBagiNCAYRAAPEI-202_1.fq.gz RS1-F11B-23_FCC4C2AACXX_L4_WHZEBagiNCAZRAAPEI-203_1.fq.gz RS1-F11B-27_FCC4C2AACXX_L4_WHZEBagiNCBARAAPEI-205_1.fq.gz RS1-F11B-29_FCC4C2AACXX_L4_WHZEBagiNCBBRAAPEI-206_1.fq.gz	fastq fastq fastq fastq	11947679555.0	243830195.0	RS1 F11B 21 FCC4C2AACXX L3 WHZEBagiNCAYRAAPEI 202 1.fq.gz	0:49	A:3159477117;C:2827401119;G:2753495798;T:3206143470;N:1162051	49		3159477117	2827401119	2753495798	3206143470	1162051	SRX2765557	SRS2149760	SRA557107	University of Turku\|Biology	University of Turku	1	0.87877		0.04488		0.77445		0.50852		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
42192	42192	SRR5482142	SRX2765556	SRS2149761	SRP105243	PRJNA383986	Danio rerio Raw sequence reads	PRJNA383986	Other	The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.		Danio rerio: Random harvested line biological replicate 2 F11 offspring originating from wild caught population	RS2 F11	breed:missing\|dev stage:juvenile\|sex:female\|tissue:liver\|death date:2014\|BioSampleModel:Model organism or animal	RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals	RS2 F11	RS2 F11	Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer. Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP105243	RS2-F11B-34_FCC4CMHACXX_L3_WHZEBagiNCBJRABPEI-214_1.fq.gz RS2-F11B-36_FCC4CMHACXX_L3_WHZEBagiNCBKRABPEI-215_1.fq.gz RS2-F11B-38_FCC4BY1ACXX_L1_WHZEBagiNCBLRABPEI-216_1.fq.gz RS2-F11B-40_FCC4BY1ACXX_L1_WHZEBagiNCBMRABPEI-218_1.fq.gz	fastq fastq fastq fastq	10619740698.0	216729402.0	RS2 F11B 38 FCC4BY1ACXX L1 WHZEBagiNCBLRABPEI 216 1.fq.gz	0:49	A:2799661065;C:2501316593;G:2465115836;T:2852970598;N:676606	49		2799661065	2501316593	2465115836	2852970598	676606	SRX2765556	SRS2149761	SRA557107	University of Turku\|Biology	University of Turku	1	0.8851		0.04865		0.80407		0.54962		49		B		usable mapping rate	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Finland	2017-12-04	Juvenile	Juvenile	Liver	Liver and Biliary System
45031	45031	SRR6466455	SRX3556412	SRS2829760	SRP128941	PRJNA428924	Danio rerio breed:TU Transcriptome or Gene expression	PRJNA428924	Transcriptome Analysis	In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish	pooled of 15 intestine of juveniles at 35 dpf old.		Control 35	breed:TU\|age:35 dpf\|sex:pooled male and female\|tissue:intestine\|treatment:Control\|BioSampleModel:Model organism or animal	RNA seq of zebrafish larvae with or without xxx administration	Ctl 35	Ctl 35	Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP128941	ZFGCK_1.fq.gz ZFGCK_2.fq.gz	fastq fastq	4031784000.0	16127136.0	ZFGCK 2.fq.gz	0:125 1:125	A:1069662566;C:940723613;G:944143624;T:1077192856;N:61341	125	125	1069662566	940723613	944143624	1077192856	61341	SRX3556412	SRS2829760	SRA646164	Chinese Academy of Agricultural Sciences\|Key Laboratory for Feed Biotechnology of the Minis	Chinese Academy of Agricultural Sciences	2	0.93591	0.9405	0.06779	0.06732	0.72157	0.72372	0.53789	0.52813	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2018-01-12	Juvenile	Juvenile	Gut	Digestive System
45032	45032	SRR6466456	SRX3556411	SRS2829759	SRP128941	PRJNA428924	Danio rerio breed:TU Transcriptome or Gene expression	PRJNA428924	Transcriptome Analysis	In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish	pooled of 15 intestine of juveniles at 35 dpf old with BL23 administration		BL23 35	breed:TU\|age:35 dpf\|sex:pooled male and female\|tissue:intestine\|treatment:BL23 administration\|BioSampleModel:Model organism or animal	RNA seq of zebrafish larvae with or without xxx administration	BL23 35	BL23 35	Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2000	SRP128941	ZFGBL23_1.fq.gz ZFGBL23_2.fq.gz	fastq fastq	3545702250.0	14182809.0	ZFGBL23 1.fq.gz	0:125 1:125	A:931928697;C:835347026;G:838503871;T:939869548;N:53108	125	125	931928697	835347026	838503871	939869548	53108	SRX3556411	SRS2829759	SRA646164	Chinese Academy of Agricultural Sciences\|Key Laboratory for Feed Biotechnology of the Minis	Chinese Academy of Agricultural Sciences	2	0.94166	0.94611	0.05678	0.05657	0.71652	0.71894	0.51987	0.53609	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2018-01-12	Juvenile	Juvenile	Gut	Digestive System
60599	60599	SRR12432918	SRX8928709	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	WT2	5	5	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraWT2_1.fq.gz egfraWT2_2.fq.gz	fastq fastq	4505046300.0	15016821.0	egfraWT2 1.fq.gz	0:150 1:150	A:1178064156;C:1082694104;G:1073742824;T:1169756132;N:789084	150	150	1178064156	1082694104	1073742824	1169756132	789084	SRX8928709	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.89561	0.8985	0.02356	0.02385	0.74383	0.74953	0.47901	0.47332	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
60600	60600	SRR12432919	SRX8928708	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	WT1	4	4	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraWT1_2.fq.gz egfraWT1_1.fq.gz	fastq fastq	4315818300.0	14386061.0	egfraWT1 1.fq.gz	0:150 1:150	A:1130385340;C:1035711280;G:1025882601;T:1123083064;N:756015	150	150	1130385340	1035711280	1025882601	1123083064	756015	SRX8928708	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.90084	0.90364	0.02361	0.0238	0.73941	0.74452	0.4717	0.47805	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
60601	60601	SRR12432920	SRX8928707	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	KO3	3	3	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraKO3_2.fq.gz egfraKO3_1.fq.gz	fastq fastq	8905879200.0	29686264.0	egfraKO3 1.fq.gz	0:150 1:150	A:2348479134;C:2123503765;G:2100165882;T:2332167190;N:1563229	150	150	2348479134	2123503765	2100165882	2332167190	1563229	SRX8928707	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.89938	0.90015	0.02459	0.02443	0.73959	0.74619	0.47427	0.48032	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
60602	60602	SRR12432921	SRX8928706	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	KO2	2	2	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraKO2_1.fq.gz egfraKO2_2.fq.gz	fastq fastq	8150314500.0	27167715.0	egfraKO2 1.fq.gz	0:150 1:150	A:2142556905;C:1947068596;G:1929502017;T:2129761480;N:1425502	150	150	2142556905	1947068596	1929502017	2129761480	1425502	SRX8928706	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.89813	0.89911	0.0236	0.0243	0.74562	0.75097	0.47766	0.48014	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
60603	60603	SRR12432922	SRX8928705	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	KO1	1	1	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraKO1_1.fq.gz egfraKO1_2.fq.gz	fastq fastq	8737229100.0	29124097.0	egfraKO1 1.fq.gz	0:150 1:150	A:2303932995;C:2082372983;G:2062052221;T:2287339032;N:1531869	150	150	2303932995	2082372983	2062052221	2287339032	1531869	SRX8928705	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.89994	0.9013	0.02483	0.02509	0.74497	0.7511	0.47316	0.4729	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
60604	60604	SRR12432923	SRX8928704	SRS7184991	SRP277140	PRJNA656674	EGFR mutant Danio rerio ovary raw sequence reads	PRJNA656674	Whole Genome Sequencing	The ovaries of 45 dpf zebrafish were separated. Transcriptome analysis between EGFR mutant and wildtype zebrafish was conducted in this project.	The zebrafish ovaries isolated from 45 dpf female were analyzed.	Ovary of 45 dpf Danio rerio	zebrafish	strain:AB\|age:45 dpf\|dev stage:puberty\|sex:female\|tissue:ovary\|BioSampleModel:Model organism or animal	WT3	6	6	common method	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina iSeq 100	SRP277140	egfraWT3_1.fq.gz egfraWT3_2.fq.gz	fastq fastq	4200074700.0	14000249.0	egfraWT3 1.fq.gz	0:150 1:150	A:1106327217;C:1001998393;G:992359377;T:1098651320;N:738393	150	150	1106327217	1001998393	992359377	1098651320	738393	SRX8928704	SRS7184991	SRA1111906	Faculty of Health Sciences, University of Macau\|Centre of Reproduction, Development and Aging	Faculty of Health Sciences, University of Macau	2	0.89695	0.90079	0.02495	0.0254	0.74304	0.74795	0.47396	0.48144	150	150	B	B	biological fallback assumption	illumina	miseq	unknown	other	unknown	bulk	unknown	unknown	China	2020-08-12	Juvenile	Juvenile	Gonad	Reproductive System
66710	66710	SRR16378894	SRX12656337	SRS10609555	SRP341786	PRJNA772011	Spatial transcriptome of zebrafish trunk section	PRJNA772011	Other	Spatial transcriptome sequencing data from sections of adult and larvae zebrafish trunk. Aiming to delineate the distribution of fast and slow muscle fibers in zebrafish by transcriptomic patterns and the regulation of muscle growth.			zebrafish larvae	strain:Riken wide type\|age:1 month\|sex:not applicable\|tissue:muscle\|birth location:Tokyo Japan\|collection date:2020 08 20\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio: larvae muscle	zebrafish larva	zebrafish larva	Visium spatial transcriptomics	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	HiSeq X Ten	SRP341786	zebra_young_S1_L004_R1_001.fastq zebra_young_S1_L004_R2_001.fastq	fastq fastq	2755287020.0	23349890.0	zebra young S1 L004 R1 001.fastq	0:28 1:90	A:775062912;C:621131964;G:654720744;T:704362634;N:8766	28	90	775062912	621131964	654720744	704362634	8766	SRX12656337	SRS10609555	SRA1312274	The University of Tokyo\|Graduate School of Agriculture and Life Science	The University of Tokyo	2	0.00167	0.91629	0.0005	0.02744	0.99707	0.85989	0.57777	0.51307	28	90	T	B	sc-like readlen	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown	Japan	2021-10-17	Juvenile	Juvenile	Muscle	Muscular System
66831	66831	SRR16674680	SRX12875367	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B8	B8	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B8.R1.fastq.gz B8.R2.fastq.gz	fastq fastq	6730442668.0	22286234.0	B8.R1.fastq.gz	0:151 1:151	A:1861252434;C:1503025278;G:1520846977;T:1845259260;N:58719	151	151	1861252434	1503025278	1520846977	1845259260	58719	SRX12875367	SRS10818487			Children's Hospital of Fudan University	2	0.94017	0.93241	0.13042	0.12914	0.68958	0.69132	0.48508	0.48284	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66832	66832	SRR16674681	SRX12875366	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B5	B5	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B5.R1.fastq.gz B5.R2.fastq.gz	fastq fastq	7110747040.0	23545520.0	B5.R1.fastq.gz	0:151 1:151	A:1977355863;C:1580608625;G:1601936422;T:1950785340;N:60790	151	151	1977355863	1580608625	1601936422	1950785340	60790	SRX12875366	SRS10818487			Children's Hospital of Fudan University	2	0.93839	0.92891	0.1351	0.13386	0.69175	0.69424	0.49143	0.49249	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66833	66833	SRR16674682	SRX12875365	SRS10818487	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain nde1KO	strain:nde1KO\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of nde1 ko Danio rerio brain	B2	B2	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B2.R1.fastq.gz B2.R2.fastq.gz	fastq fastq	8547028538.0	28301419.0	B2.R1.fastq.gz	0:151 1:151	A:2378598350;C:1891330158;G:1921569124;T:2355455648;N:75258	151	151	2378598350	1891330158	1921569124	2355455648	75258	SRX12875365	SRS10818487			Children's Hospital of Fudan University	2	0.94029	0.92534	0.13616	0.13373	0.68949	0.69219	0.47948	0.48398	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66834	66834	SRR16674683	SRX12875364	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B7	B7	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B7.R1.fastq.gz B7.R2.fastq.gz	fastq fastq	6685388496.0	22137048.0	B7.R1.fastq.gz	0:151 1:151	A:1860264075;C:1483831512;G:1503216220;T:1838014556;N:62133	151	151	1860264075	1483831512	1503216220	1838014556	62133	SRX12875364	SRS10818488			Children's Hospital of Fudan University	2	0.94254	0.93341	0.13834	0.13689	0.69355	0.69755	0.49201	0.49217	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66835	66835	SRR16674684	SRX12875363	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B4	B4	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B4.R1.fastq.gz B4.R2.fastq.gz	fastq fastq	7546711220.0	24989110.0	B4.R1.fastq.gz	0:151 1:151	A:2099092660;C:1670910951;G:1699960602;T:2076680479;N:66528	151	151	2099092660	1670910951	1699960602	2076680479	66528	SRX12875363	SRS10818488			Children's Hospital of Fudan University	2	0.94254	0.92745	0.13347	0.13114	0.69225	0.69424	0.48413	0.49124	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-01	Juvenile	Juvenile	Brain	Nervous System
66836	66836	SRR16674685	SRX12875362	SRS10818488	SRP343978	PRJNA776712	RNA seq analysis of nde1 mutant zebrafish	PRJNA776712	Other	We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.			brain WT	strain:TU\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio brain	B1	B1	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP343978	B1.R1.fastq.gz B1.R2.fastq.gz	fastq fastq	6758464342.0	22379021.0	B1.R1.fastq.gz	0:151 1:151	A:1881676275;C:1495234309;G:1519420774;T:1862074223;N:58761	151	151	1881676275	1495234309	1519420774	1862074223	58761	SRX12875362	SRS10818488			Children's Hospital of Fudan University	2	0.94263	0.92421	0.13676	0.13324	0.69505	0.697	0.48389	0.48239	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2021-11-02	Juvenile	Juvenile	Brain	Nervous System
68554	68554	SRR18010263	SRX14164590	SRS11988750	SRP359660	PRJNA806676	Transcriptome analysis of nomo1 homologous deficiency zebrafish	PRJNA806676	Other	This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.			nomo1	strain:nomo / \|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rario: nomo1	nomo	nomo	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP359660	NOMO_1.fq.gz NOMO_2.fq.gz	fastq fastq	7423945800.0	24746486.0	NOMO 1.fq.gz	0:150 1:150	A:2079187833;C:1643658691;G:1652867282;T:2048199003;N:32991	150	150	2079187833	1643658691	1652867282	2048199003	32991	SRX14164590	SRS11988750			Children's Hospital of Fudan University	2	0.93796	0.93625	0.16379	0.1632	0.69643	0.69842	0.48865	0.48976	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2022-02-13	Juvenile	Juvenile	Brain	Nervous System
68555	68555	SRR18010264	SRX14164589	SRS11988749	SRP359660	PRJNA806676	Transcriptome analysis of nomo1 homologous deficiency zebrafish	PRJNA806676	Other	This analysis revealed transcriptome level changes of brain of nomo1 homologous deficiency zebrafish.			WT	strain:tu\|dev stage:2mpf\|sex:male\|tissue:brain\|BioSampleModel:Model organism or animal	RNA seq of Danio rario: TU	TU	TU	RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego CA using 5g of total RNA. Shortly messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen CA with random hexamer primers Illumina. Then the synthesized cDNA was subjected to end repair phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380 paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2 150bp read length.	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP359660	TU_1.fq.gz TU_2.fq.gz	fastq fastq	7981027200.0	26603424.0	TU 1.fq.gz	0:150 1:150	A:2246332345;C:1756444706;G:1767372264;T:2210842856;N:35029	150	150	2246332345	1756444706	1767372264	2210842856	35029	SRX14164589	SRS11988749			Children's Hospital of Fudan University	2	0.93375	0.93291	0.17081	0.17028	0.69755	0.69875	0.48942	0.49405	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2022-02-13	Juvenile	Juvenile	Brain	Nervous System

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