metadata: run_metadata: 27 rows where experiment.library_selection = "PolyA" and tissue

27 rows where experiment.library_selection = "PolyA" and tissue_curation = "Multi-tissue"

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.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
175	175	DRR084197	DRX078028	DRS086522	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		natural paring early sample	zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2]	SAMD00073604		sample name:M 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073604	DRX078028	zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073604				1389837888.0	38606608.0	DRR084197	0:36	A:320671418;C:336948866;G:347550258;T:381720581;N:2946765	36		320671418	336948866	347550258	381720581	2946765	DRX078028	DRS086522	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89763		0.02235		0.76445		0.46381		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Zygote	Embryo	Multi-tissue	Multi-system
181	181	DRR084191	DRX078022	DRS086516	DRP004758	PRJDB5490	Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish	DRP004758	Other	Two essential processes oocyte maturation and ovulation before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid 17 20 beta dihydroxy 4 pregnen 3 one 17 20 beta DHP in teleost the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.		natural paring early sample	zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1]	SAMD00073598		sample name:M\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073598	DRX078022	zebrafish ovary isolated from adult fish natural paring oocyte maturation. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit		RNA-Seq	TRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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>	DRP004758	Illumina HiSeq 2500 sequencing of SAMD00073598				1050981012.0	29193917.0	DRR084191	0:36	A:241048832;C:256186268;G:260277071;T:293299597;N:169244	36		241048832	256186268	260277071	293299597	169244	DRX078022	DRS086516	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.9088		0.02369		0.7624		0.47998		36		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Zygote	Embryo	Multi-tissue	Multi-system
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
10147	10147	ERR5005147	ERX4814430	ERS5474667	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	6wpf rep2 RNA	SAMEA7727294	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727294\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:6wpf rep2 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:6wpf rep2 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:6wpf rep2 RNA p	6wpf rep2 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	6wpf_rep2_RNA_R1.fastq.gz 6wpf_rep2_RNA_R2.fastq.gz	fastq fastq	11929324428.0	40157012.0	E MTAB 9924:6wpf rep2 RNA R	0:148.72 1:148.34	A:3237937670;C:2713313024;G:2724528618;T:3251908184;N:1636932	148	148	3237937670	2713313024	2724528618	3251908184	1636932	ERX4814430	ERS5474667	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.93069	0.93326	0.13891	0.13708	0.69779	0.71701	0.49797	0.49993	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
10148	10148	ERR5005146	ERX4814429	ERS5474666	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	6wpf rep1 RNA	SAMEA7727293	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727293\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:6wpf rep1 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:6wpf rep1 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:6wpf rep1 RNA p	6wpf rep1 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	6wpf_rep1_RNA_R1.fastq.gz 6wpf_rep1_RNA_R2.fastq.gz	fastq fastq	19633084666.0	66362913.0	E MTAB 9924:6wpf rep1 RNA R	0:148.10 1:147.74	A:5348913370;C:4443593237;G:4456508875;T:5380825384;N:3243800	148	147	5348913370	4443593237	4456508875	5380825384	3243800	ERX4814429	ERS5474666	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.92182	0.92338	0.12138	0.11866	0.68499	0.70236	0.50638	0.51742	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
10149	10149	ERR5005145	ERX4814428	ERS5474665	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	adult rep2 RNA	SAMEA7727292	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727292\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:adult rep2 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:adult rep2 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:adult rep2 RNA p	adult rep2 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	adult_rep2_RNA_R1.fastq.gz adult_rep2_RNA_R2.fastq.gz	fastq fastq	15648506033.0	52770962.0	E MTAB 9924:adult rep2 RNA R	0:148.45 1:148.09	A:4268818428;C:3540462921;G:3548332979;T:4288409679;N:2482026	148	148	4268818428	3540462921	3548332979	4288409679	2482026	ERX4814428	ERS5474665	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.94625	0.94771	0.13596	0.1321	0.691	0.70709	0.53016	0.5357	148	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Adult	Adult	Multi-tissue	Multi-system
10150	10150	ERR5005144	ERX4814427	ERS5474664	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	adult rep1 RNA	SAMEA7727291	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727291\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:adult rep1 RNA\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:adult rep1 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:adult rep1 RNA p	adult rep1 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:6\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	adult_rep1_RNA_R1.fastq.gz adult_rep1_RNA_R2.fastq.gz	fastq fastq	12526662412.0	42363955.0	E MTAB 9924:adult rep1 RNA R	0:148.02 1:147.67	A:3489175783;C:2756879350;G:2771544913;T:3507538808;N:1523558	148	147	3489175783	2756879350	2771544913	3507538808	1523558	ERX4814427	ERS5474664	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.94246	0.94448	0.14788	0.14431	0.70065	0.7181	0.50361	0.50894	149	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Adult	Adult	Multi-tissue	Multi-system
10151	10151	ERR5005143	ERX4814426	ERS5474663	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	4wpf rep2 RNA	SAMEA7727290	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727290\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:4wpf rep2 RNA\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:4wpf rep2 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:4wpf rep2 RNA p	4wpf rep2 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:4\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	4wpf_rep2_RNA_R1.fastq.gz 4wpf_rep2_RNA_R2.fastq.gz	fastq fastq	17862998816.0	62733750.0	E MTAB 9924:4wpf rep2 RNA R	0:142.46 1:142.28	A:4963776868;C:3947656384;G:3887833339;T:5057912943;N:5819282	142	142	4963776868	3947656384	3887833339	5057912943	5819282	ERX4814426	ERS5474663	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.9309	0.93111	0.1952	0.1951	0.70534	0.7176	0.50482	0.51152	116	147	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
10152	10152	ERR5005142	ERX4814425	ERS5474662	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	4wpf rep1 RNA	SAMEA7727289	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727289\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:4wpf rep1 RNA\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:4wpf rep1 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:4wpf rep1 RNA p	4wpf rep1 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:4\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	4wpf_rep1_RNA_R1.fastq.gz 4wpf_rep1_RNA_R2.fastq.gz	fastq fastq	17991275539.0	62100394.0	E MTAB 9924:4wpf rep1 RNA R	0:144.97 1:144.75	A:5021314085;C:3954412393;G:3881029269;T:5128240171;N:6279621	144	144	5021314085	3954412393	3881029269	5128240171	6279621	ERX4814425	ERS5474662	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.92732	0.92708	0.18879	0.18795	0.70171	0.71634	0.506	0.50887	150	149	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
10153	10153	ERR5005141	ERX4814424	ERS5474661	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	3wpf rep2 RNA	SAMEA7727288	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727288\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:3wpf rep2 RNA\|age:3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:3wpf rep2 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:3wpf rep2 RNA p	3wpf rep2 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:3\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	3wpf_rep2_RNA_R1.fastq.gz 3wpf_rep2_RNA_R2.fastq.gz	fastq fastq	22804042203.0	76957632.0	E MTAB 9924:3wpf rep2 RNA R	0:148.34 1:147.98	A:6255991654;C:5120232312;G:5136799470;T:6288581486;N:2437281	148	147	6255991654	5120232312	5136799470	6288581486	2437281	ERX4814424	ERS5474661	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.93211	0.93322	0.20907	0.2056	0.6983	0.71652	0.53448	0.5352	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
10154	10154	ERR5005140	ERX4814423	ERS5474660	ERP125923	PRJEB42059	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E-MTAB-9924	Other	DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes however non CG methylation mCH is also detectable in vertebrate tissues most notably in the nervous system. In mammalian brains it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A ii enriched in gene bodies and repetitive elements and iii associated with transcriptional repression. However the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	3wpf rep1 RNA	SAMEA7727287	Genomics and Epigenetics Division, Garvan Institute of Medical Research,	ENA first public:2020 12 18\|ENA last update:2020 12 17\|External Id:SAMEA7727287\|INSDC center alias:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC center name:Genomics and Epigenetics Division Garvan Institute of Medical Research \|INSDC first public:2020 12 18T17:06:48Z\|INSDC last update:2020 12 17T08:36:39Z\|INSDC status:public\|Submitter Id:E MTAB 9924:3wpf rep1 RNA\|age:3\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval stage\|genotype:wild type genotype\|individual:5\|organism part:brain\|sample name:E MTAB 9924:3wpf rep1 RNA\|sex:mixed\|strain:Mixed AB and Tubingen	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	E MTAB 9924:3wpf rep1 RNA p	3wpf rep1 RNA p	RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at 80°C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN Chadstone VIC Australia according to manufacturer instructions. For RNA extraction half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit according to the manufacturer's instructions.	Experimental Factor: age:3\|Experimental Factor: genotype:wild type genotype\|Experimental Factor: protocol:RNA Seq	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	HiSeq X Ten		ERP125923	HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain	ENA FIRST PUBLIC:2020 12 18\|ENA LAST UPDATE:2020 12 17	3wpf_rep1_RNA_R1.fastq.gz 3wpf_rep1_RNA_R2.fastq.gz	fastq fastq	25549987003.0	86260528.0	E MTAB 9924:3wpf rep1 RNA R	0:148.28 1:147.91	A:6961927451;C:5786809647;G:5798882444;T:6999483818;N:2883643	148	147	6961927451	5786809647	5798882444	6999483818	2883643	ERX4814423	ERS5474660	ERA3199751	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	Genomics and Epigenetics Division, Garvan Institute of Medical Research,\|European Nucleotide Archive	2	0.93267	0.93467	0.20372	0.20263	0.69252	0.70962	0.53426	0.54087	149	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2020-12-17	Larval	Larval	Multi-tissue	Multi-system
28882	28882	SRR26783947	SRX22482174	SRS19495555	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #2		isolate:UAS::GFP control #2\|age:9 month 16 month\|collection date:2023 01 12\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #2	A10	A10	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A10_EKRN230034972-1A_HHG75DSX7_L2_2.fq.gz A10_EKRN230034972-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	7982890500.0	26609635.0	A10 EKRN230034972 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2129699297;C:1884782648;G:1870728993;T:2097648646;N:30916	150	150	2129699297	1884782648	1870728993	2097648646	30916	SRX22482174	SRS19495555	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93382	0.93397	0.06505	0.06535	0.69826	0.69875	0.51693	0.51829	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28883	28883	SRR26783948	SRX22482173	SRS19495553	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #1		isolate:UAS::GFP control #1\|age:9 month 16 month\|collection date:2023 01 11\|geo loc name:Finland: Tampere Europe\|sex:male\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #1	A9	A9	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A9_EKRN230034971-1A_HHG75DSX7_L2_1.fq.gz A9_EKRN230034971-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	6119764500.0	20399215.0	A9 EKRN230034971 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1652919782;C:1426521039;G:1415190390;T:1625109104;N:24185	150	150	1652919782	1426521039	1415190390	1625109104	24185	SRX22482173	SRS19495553	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93503	0.93495	0.07197	0.07148	0.71995	0.71973	0.5119	0.51499	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28884	28884	SRR26783949	SRX22482172	SRS19495554	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #8		isolate:ETV6::RUNX1 knock in zebrafish #8\|age:9 month 16 month\|collection date:2023 05 10\|geo loc name:Finland: Tampere Europe\|sex:male\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #8	A8	A8	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A8_EKRN230034970-1A_HHG75DSX7_L2_1.fq.gz A8_EKRN230034970-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7920658200.0	26402194.0	A8 EKRN230034970 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2084803636;C:1894755310;G:1880741705;T:2060327167;N:30382	150	150	2084803636	1894755310	1880741705	2060327167	30382	SRX22482172	SRS19495554	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93929	0.94055	0.10937	0.1102	0.71741	0.71756	0.46004	0.46358	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28885	28885	SRR26783950	SRX22482171	SRS19495552	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #7		isolate:ETV6::RUNX1 knock in zebrafish #7\|age:9 month 16 month\|collection date:2023 03 09\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #7	A7	A7	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A7_EKRN230034969-1A_HHG75DSX7_L2_2.fq.gz A7_EKRN230034969-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	8875539300.0	29585131.0	A7 EKRN230034969 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2426453238;C:2049446891;G:2017593291;T:2382011570;N:34310	150	150	2426453238	2049446891	2017593291	2382011570	34310	SRX22482171	SRS19495552	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.92101	0.92052	0.12337	0.12369	0.74052	0.74012	0.47692	0.47624	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28886	28886	SRR26783951	SRX22482170	SRS19495551	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #6		isolate:ETV6::RUNX1 knock in zebrafish #6\|age:9 month 16 month\|collection date:2023 03 08\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #6	A6	A6	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A6_EKRN230034968-1A_HHG75DSX7_L2_1.fq.gz A6_EKRN230034968-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7560052500.0	25200175.0	A6 EKRN230034968 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2044845958;C:1762698184;G:1744547769;T:2007930943;N:29646	150	150	2044845958	1762698184	1744547769	2007930943	29646	SRX22482170	SRS19495551	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.92673	0.92704	0.11586	0.1157	0.73464	0.73454	0.49457	0.49107	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28887	28887	SRR26783952	SRX22482169	SRS19495550	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #5		isolate:ETV6::RUNX1 knock in zebrafish #5\|age:9 month 16 month\|collection date:2023 03 07\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #5	A5	A5	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A5_EKRN230034967-1A_HHG75DSX7_L2_1.fq.gz A5_EKRN230034967-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	8269320000.0	27564400.0	A5 EKRN230034967 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2208684304;C:1954270073;G:1933348989;T:2172985012;N:31622	150	150	2208684304	1954270073	1933348989	2172985012	31622	SRX22482169	SRS19495550	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.94285	0.9422	0.08987	0.08977	0.75507	0.7541	0.52032	0.50956	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28888	28888	SRR26783953	SRX22482168	SRS19495549	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #4		isolate:ETV6::RUNX1 knock in zebrafish #4\|age:9 month 16 month\|collection date:2023 02 06\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #4	A4	A4	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A4_EKRN230034966-1A_HHG75DSX7_L2_2.fq.gz A4_EKRN230034966-1A_HHG75DSX7_L2_1.fq.gz	fastq fastq	6514998000.0	21716660.0	A4 EKRN230034966 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1755226695;C:1525196740;G:1509297214;T:1725251790;N:25561	150	150	1755226695	1525196740	1509297214	1725251790	25561	SRX22482168	SRS19495549	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93241	0.93171	0.08147	0.08039	0.72318	0.72271	0.48554	0.48715	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28889	28889	SRR26783954	SRX22482167	SRS19495548	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #3		isolate:ETV6::RUNX1 knock in zebrafish #3\|age:9 month 16 month\|collection date:2023 02 05\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #3	A3	A3	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A3_EKRN230034965-1A_HHG75DSX7_L2_1.fq.gz A3_EKRN230034965-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7439426700.0	24798089.0	A3 EKRN230034965 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:1997063524;C:1750471227;G:1730255985;T:1961607399;N:28565	150	150	1997063524	1750471227	1730255985	1961607399	28565	SRX22482167	SRS19495548	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93247	0.93234	0.10911	0.10805	0.73359	0.73377	0.49804	0.4981	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28890	28890	SRR26783955	SRX22482166	SRS19495547	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				Non leukemic kidney marrow control #3		isolate:UAS::GFP control #3\|age:9 month 16 month\|collection date:2023 01 13\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: non leukemic whole kidney marrow #3	A11	A11	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A11_EKRN230034973-1A_HHG75DSX7_L2_1.fq.gz A11_EKRN230034973-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	7535572200.0	25118574.0	A11 EKRN230034973 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2030032446;C:1757927547;G:1745325371;T:2002258226;N:28610	150	150	2030032446	1757927547	1745325371	2002258226	28610	SRX22482166	SRS19495547	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93698	0.93781	0.07017	0.0697	0.72324	0.72316	0.52767	0.52695	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28891	28891	SRR26783956	SRX22482165	SRS19495546	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #2		isolate:ETV6::RUNX1 knock in zebrafish #2\|age:9 month 16 month\|collection date:2023 01 04\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #2	A2	A2	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A2_EKRN230034964-1A_HHG75DSX7_L2_1.fq.gz A2_EKRN230034964-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	8139110700.0	27130369.0	A2 EKRN230034964 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2200986080;C:1900110630;G:1876627982;T:2161354090;N:31918	150	150	2200986080	1900110630	1876627982	2161354090	31918	SRX22482165	SRS19495546	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93418	0.93374	0.11817	0.11792	0.73227	0.73251	0.49375	0.49338	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	Adult	Adult	Multi-tissue	Multi-system
28892	28892	SRR26783957	SRX22482164	SRS19495545	SRP471222	PRJNA1038711	Zebrafish leukemia sequencing	PRJNA1038711	Other	Validation of an ETV6::RUNX1 positive pB ALL zebrafish model				ETV6::RUNX1 tumor #1		isolate:ETV6::RUNX1 knock in zebrafish #1\|age:9 month 16 month\|collection date:2023 01 03\|geo loc name:Finland: Tampere Europe\|sex:female\|tissue:Kidney marrow\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: leukemic whole kidney marrow #1	A1	A1	PCR			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq X		SRP471222			A1_EKRN230034963-1A_HHG75DSX7_L2_1.fq.gz A1_EKRN230034963-1A_HHG75DSX7_L2_2.fq.gz	fastq fastq	10375495200.0	34584984.0	A1 EKRN230034963 1A HHG75DSX7 L2 1.fq.gz	0:150 1:150	A:2781268558;C:2442675432;G:2417292722;T:2734218470;N:40018	150	150	2781268558	2442675432	2417292722	2734218470	40018	SRX22482164	SRS19495545	SRA1748743	Tampere University\|Clinical Medicine	Tampere University	2	0.93836	0.93801	0.12376	0.12224	0.74416	0.74406	0.49065	0.48915	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Finland	2023-11-10	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");;