metadata: run_metadata: 6 rows where experiment.library_selection = "PolyA", technology = "bulk" and tissue_curation

6 rows where experiment.library_selection = "PolyA", technology = "bulk" and tissue_curation_coarse = "Multi-system"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
9702	9702	ERR3301003	ERX3327070	ERS3389658	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 3	SAMEA5585434	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585434\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 3\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:6\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 3\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 3 p	WT heart rep 3 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz	fastq fastq	7339830080.0	45873938.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3	0:80 1:80	A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141	80	80	1985328994	1673818891	1695753386	1984031668	897141	ERX3327070	ERS3389658	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.9311	0.94858	0.07774	0.07789	0.76378	0.76394	0.52815	0.52065	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9703	9703	ERR3301002	ERX3327069	ERS3389657	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 2	SAMEA5585433	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585433\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 2\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:5\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 2\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 2 p	WT heart rep 2 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz	fastq fastq	7486415840.0	46790099.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2	0:80 1:80	A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493	80	80	2020798219	1702752807	1731176796	2030756525	931493	ERX3327069	ERS3389657	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93397	0.9509	0.07752	0.07859	0.76019	0.76002	0.54034	0.54728	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9704	9704	ERR3301001	ERX3327068	ERS3389656	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	WT heart rep 1	SAMEA5585432	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:47Z\|External Id:SAMEA5585432\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:47Z\|INSDC status:public\|Submitter Id:E MTAB 7920:WT heart rep 1\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:normal\|genotype:wild type genotype\|individual:4\|organism part:heart\|sample name:E MTAB 7920:WT heart rep 1\|scientific name:Danio rerio\|sex:female\|strain:AB	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:WT heart rep 1 p	WT heart rep 1 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:wild type genotype\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz	fastq fastq	6814600800.0	42591255.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1	0:80 1:80	A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985	80	80	1823108307	1567497576	1587567005	1835589927	837985	ERX3327068	ERS3389656	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93109	0.94806	0.07581	0.07635	0.75907	0.75988	0.54746	0.54753	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9708	9708	ERR3300997	ERX3327064	ERS3389652	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 3	SAMEA5585428	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585428\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 3\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:3\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 3\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 3 p	Mutant heart rep 3 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz	fastq fastq	7240447520.0	45252797.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3	0:80 1:80	A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957	80	80	1968283412	1645458614	1652590010	1973242527	872957	ERX3327064	ERS3389652	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.92784	0.94597	0.08601	0.08686	0.76702	0.76449	0.50929	0.52685	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9709	9709	ERR3300996	ERX3327063	ERS3389651	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 2	SAMEA5585427	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:03Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585427\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:03Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 2\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:2\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 2\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 2 p	Mutant heart rep 2 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz	fastq fastq	7347029600.0	45918935.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2	0:80 1:80	A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229	80	80	1967915665	1690507331	1712776156	1974918219	912229	ERX3327063	ERS3389651	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93337	0.94978	0.07673	0.07724	0.76755	0.76798	0.53415	0.51157	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-system
9710	9710	ERR3300995	ERX3327062	ERS3389650	ERP115040	PRJEB32363	RNA seq of zebrafish sa12692 mutants against WT controls	E-MTAB-7920	Transcriptome Analysis	Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages.	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th…	Mutant heart rep 1	SAMEA5585426	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway	ENA FIRST PUBLIC:2021 04 30T00:25:02Z\|ENA LAST UPDATE:2019 04 30T15:21:46Z\|External Id:SAMEA5585426\|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway\|INSDC first public:2021 04 30T00:25:02Z\|INSDC last update:2019 04 30T15:21:46Z\|INSDC status:public\|Submitter Id:E MTAB 7920:Mutant heart rep 1\|age:1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|disease:Naxos disease\|genotype:sa12692 mutant\|individual:1\|organism part:heart\|sample name:E MTAB 7920:Mutant heart rep 1\|scientific name:Danio rerio\|sex:female\|strain:sa12692 mutant	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	E MTAB 7920:Mutant heart rep 1 p	Mutant heart rep 1 p	RNA seq of zebrafish sa12692 mutants against WT controls	Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T…	Experimental Factor: genotype:sa12692 mutant\|Experimental Factor: developmental stage:adult\|Experimental Factor: organism part:heart	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	ERP115040	NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls	ENA FIRST PUBLIC:2021 04 30\|ENA LAST UPDATE:2019 04 30	HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz	fastq fastq	6296502880.0	39353143.0	E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1	0:80 1:80	A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941	80	80	1677737687	1460767489	1468915029	1688319734	762941	ERX3327062	ERS3389650	ERA1880314	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway\|European Nucleotide Archive	2	0.93775	0.9516	0.07994	0.08077	0.75844	0.75759	0.51937	0.52207	80	80	B	B	biological fallback assumption	illumina	nextseq	3prime	poly_a	trueseq	bulk	bulk	bulk	Ireland	2019-04-30	Adult	Adult	Multi-tissue	Multi-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");;