metadata: run_metadata: 13 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RT-PCR" and tissue

13 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "RT-PCR" and tissue_curation = "Liver"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	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
38289	38289	SRR1731761	SRX828260	SRS807370	SRP051449	PRJNA266270	Danio rerio Transcriptome or Gene expression	PRJNA266270	Other	To identify molecular signals that initiate liver regeneration post 1/3 PH		sham operated liver transcriptome post 1/3 PH	breed:AB line\|cultivar:AB line\|strain:AB line\|age:10 month\|sex:female\|tissue:liver\|BioSampleModel:Model organism or animal	sham operated liver transcriptome post 1/3 PH	sham operated	1	1	RNA-Seq	TRANSCRIPTOMIC	RT-PCR	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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>	SRP051449	sham-operated_R1.fastq.gz sham-operated_R2.fastq.gz	fastq fastq	2339904960.0	16249340.0	sham operated	0:72 1:72	A:639730953;C:549099184;G:603489762;T:545135156;N:2449905	72	72	639730953	549099184	603489762	545135156	2449905	SRX828260	SRS807370	SRA223828	Institute of Hydrobiology, Chinese Academy of Scie\|The Key Laboratory of Aquatic Biodiversity and Con	Chinese Academy of Sciences	2	0.9353	0.91074	0.02617	0.0253	0.86334	0.86387	0.35902	0.36066	72	72	B	B	biological fallback assumption	illumina	early_illumina	unknown	other	unknown	bulk	unknown	unknown	China	2016-02-05	Adult	Adult	Liver	Liver and Biliary 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

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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");;