rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,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.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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 the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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