{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"PolyA\" and technology = \"bulk\"", "rows": [[6, "DRR315802", "DRX305194", "DRS231989", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample4", "SAMD00400823", null, "sample name:rw147 2.5dpf wildtype  rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", "DRX305194", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400823", null, null, null, 10262353995.0, 34151547.0, "DRR315802", "0:150.27 1:150.22", "A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550", 150, 150, null, null, 2735078560, 2386126821, 2433638250, 2707202814, 307550, "DRX305194", "DRS231989", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95231, 0.95295, 0.09229, 0.08773, 0.71819, 0.72107, 0.46746, 0.46617, 151, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [7, "DRR315801", "DRX305193", "DRS231988", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample3", "SAMD00400822", null, "sample name:rw147 2.5dpf wildtype  rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", "DRX305193", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400822", null, null, null, 11516368634.0, 38355888.0, "DRR315801", "0:150.15 1:150.10", "A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954", 150, 150, null, null, 3080341643, 2678048339, 2713051368, 3044449330, 477954, "DRX305193", "DRS231988", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95353, 0.95634, 0.08909, 0.08533, 0.71374, 0.71252, 0.45986, 0.46059, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [8, "DRR315800", "DRX305192", "DRS231987", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample2", "SAMD00400821", null, "sample name:rw147 2.5dpf wildtype  rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", "DRX305192", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400821", null, null, null, 8814057148.0, 29367513.0, "DRR315800", "0:150.09 1:150.04", "A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957", 150, 150, null, null, 2350403211, 2054073465, 2083044327, 2326181188, 354957, "DRX305192", "DRS231987", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95287, 0.95643, 0.0891, 0.08586, 0.70309, 0.70252, 0.46384, 0.46281, 151, 149, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [9, "DRR315799", "DRX305191", "DRS231986", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "wildtype sibling sample1", "SAMD00400820", null, "sample name:rw147 2.5dpf wildtype  rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", "DRX305191", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400820", null, null, null, 10491955578.0, 34900682.0, "DRR315799", "0:150.34 1:150.28", "A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831", 150, 150, null, null, 2796521111, 2446218287, 2483414564, 2765477785, 323831, "DRX305191", "DRS231986", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9539, 0.95646, 0.08185, 0.07808, 0.70025, 0.70013, 0.44713, 0.44987, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [10, "DRR315798", "DRX305190", "DRS231985", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample4", "SAMD00400819", null, "sample name:rw147 2.5dpf Mutant  rep 4|biological replicate:4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", "DRX305190", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400819", null, null, null, 9197802250.0, 30604326.0, "DRR315798", "0:150.30 1:150.24", "A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028", 150, 150, null, null, 2468967963, 2130949980, 2158692262, 2438931017, 261028, "DRX305190", "DRS231985", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95159, 0.95439, 0.10146, 0.09758, 0.71995, 0.71983, 0.46519, 0.46797, 150, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [11, "DRR315797", "DRX305189", "DRS231984", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample3", "SAMD00400818", null, "sample name:rw147 2.5dpf Mutant  rep 3|biological replicate:3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", "DRX305189", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400818", null, null, null, 10498982078.0, 34931731.0, "DRR315797", "0:150.31 1:150.25", "A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945", 150, 150, null, null, 2804535103, 2445295179, 2478768789, 2770066062, 316945, "DRX305189", "DRS231984", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95448, 0.95652, 0.0939, 0.0887, 0.71796, 0.71847, 0.46335, 0.46615, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [12, "DRR315796", "DRX305188", "DRS231983", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample2", "SAMD00400817", null, "sample name:rw147 2.5dpf Mutant  rep 2|biological replicate:2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", "DRX305188", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400817", null, null, null, 9850145990.0, 32782079.0, "DRR315796", "0:150.26 1:150.21", "A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024", 150, 150, null, null, 2636205537, 2286508705, 2319481100, 2607600624, 350024, "DRX305188", "DRS231983", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.95193, 0.95472, 0.09722, 0.09375, 0.7138, 0.71299, 0.45542, 0.45994, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [13, "DRR315795", "DRX305187", "DRS231982", "DRP008318", "PRJDB12206", "Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes", "DRP008318", "Transcriptome Analysis", "Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level  transcriptome of strip1 mutant \"rw147\" eye cups at 2.5 dpf was compared to that of  wild type siblings using bulk RNA sequencing analysis.", null, null, null, "strip1 mutant sample1", "SAMD00400816", null, "sample name:rw147 2.5dpf Mutant  rep 1|biological replicate:1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", "DRX305187", "1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>151</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP008318", "Illumina NovaSeq 6000 paired end sequencing of SAMD00400816", null, null, null, 9542039835.0, 31780260.0, "DRR315795", "0:150.15 1:150.10", "A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225", 150, 150, null, null, 2543384204, 2224374632, 2258183435, 2515655339, 442225, "DRX305187", "DRS231982", "DRA012640", "OIST|Developmental Neurobiology Unit", "Developmental Neurobiology Unit", 2, 0.9528, 0.95591, 0.08656, 0.0828, 0.70352, 0.70331, 0.45316, 0.44914, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Unknown", "2022-03-16", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [9699, "ERR3301006", "ERX3327073", "ERS3389661", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 3", "SAMEA5585437", "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:SAMEA5585437|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 embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 3|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:WT embryo rep 3 p", "WT embryo rep 3 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1WTembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_2.fq.gz", "fastq fastq", 7308473280.0, 45677958.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo3 ", "0:80 1:80", "A:1898812783;C:1731426486;G:1757309247;T:1920031807;N:892957", 80, 80, null, null, 1898812783, 1731426486, 1757309247, 1920031807, 892957, "ERX3327073", "ERS3389661", "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, 0.94288, 0.95671, 0.07985, 0.08023, 0.67915, 0.67815, 0.47781, 0.48461, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [9700, "ERR3301005", "ERX3327072", "ERS3389660", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 2", "SAMEA5585436", "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:SAMEA5585436|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 embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 2|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:WT embryo rep 2 p", "WT embryo rep 2 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1WTembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_2.fq.gz", "fastq fastq", 7424396000.0, 46402475.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo2 ", "0:80 1:80", "A:1940921070;C:1754354124;G:1768688429;T:1959515088;N:917289", 80, 80, null, null, 1940921070, 1754354124, 1768688429, 1959515088, 917289, "ERX3327072", "ERS3389660", "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, 0.94222, 0.95663, 0.0909, 0.09022, 0.67929, 0.67606, 0.48763, 0.48719, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [9701, "ERR3301004", "ERX3327071", "ERS3389659", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 1", "SAMEA5585435", "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:SAMEA5585435|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 embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 1|scientific name:Danio rerio|strain:AB", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:WT embryo rep 1 p", "WT embryo rep  1 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1WTembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_2.fq.gz", "fastq fastq", 7300913760.0, 45630711.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo1 ", "0:80 1:80", "A:1931507380;C:1703881934;G:1712942848;T:1951676424;N:905174", 80, 80, null, null, 1931507380, 1703881934, 1712942848, 1951676424, 905174, "ERX3327071", "ERS3389659", "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, 0.93831, 0.95401, 0.09471, 0.09526, 0.67576, 0.67403, 0.48092, 0.48297, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "Ireland", "2019-04-30", "Adult", "Adult", "Multi-tissue", "Multi-system"], [9705, "ERR3301000", "ERX3327067", "ERS3389655", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 3", "SAMEA5585431", "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:SAMEA5585431|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:Mutant embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 3|scientific name:Danio rerio|strain:sa12692 mutant", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:Mutant embryo rep 3 p", "Mutant embryo rep 3 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1Mutantembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_2.fq.gz", "fastq fastq", 6323854560.0, 39524091.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo3 ", "0:80 1:80", "A:1662088892;C:1473777430;G:1500364334;T:1686853051;N:770853", 80, 80, null, null, 1662088892, 1473777430, 1500364334, 1686853051, 770853, "ERX3327067", "ERS3389655", "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, 0.93548, 0.95404, 0.09034, 0.09103, 0.67584, 0.67592, 0.47892, 0.48193, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [9706, "ERR3300999", "ERX3327066", "ERS3389654", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 2", "SAMEA5585430", "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:SAMEA5585430|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 embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 2|scientific name:Danio rerio|strain:sa12692 mutant", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:Mutant embryo rep 2 p", "Mutant embryo rep 2 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1Mutantembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_2.fq.gz", "fastq fastq", 6564227680.0, 41026423.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo2 ", "0:80 1:80", "A:1702331829;C:1557343680;G:1583770440;T:1719974488;N:807243", 80, 80, null, null, 1702331829, 1557343680, 1583770440, 1719974488, 807243, "ERX3327066", "ERS3389654", "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, 0.94141, 0.95836, 0.07518, 0.07501, 0.67982, 0.67803, 0.47895, 0.47763, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [9707, "ERR3300998", "ERX3327065", "ERS3389653", "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", null, "Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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 embryo rep 1", "SAMEA5585429", "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:SAMEA5585429|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 embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 1|scientific name:Danio rerio|strain:sa12692 mutant", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls", "E MTAB 7920:Mutant embryo rep 1 p", "Mutant embryo rep 1 p", "RNA seq of zebrafish sa12692 mutants against WT controls", "Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol\u00ae. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "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_lane1Mutantembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_2.fq.gz", "fastq fastq", 6991429280.0, 43696433.0, "E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo1 ", "0:80 1:80", "A:1852543850;C:1630880197;G:1635963943;T:1871173669;N:867621", 80, 80, null, null, 1852543850, 1630880197, 1635963943, 1871173669, 867621, "ERX3327065", "ERS3389653", "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, 0.93819, 0.95201, 0.10106, 0.10107, 0.67541, 0.67523, 0.4792, 0.48253, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "3prime", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "Ireland", "2019-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "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", null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, null, null, null, null, null, null, null, "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\u00ae until use. All centrifugation steps for RNA extractions occurred at 4\u00b0C. RNA was extracted using the TRIzol\u00ae 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\u00ae to a 1.5 mL tube. TRIzol\u00ae 250 \u03bcL 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\u00ae 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\u00ae 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\u00ae 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 \u00b5L of nuclease free water and heated at 55\u00b0C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 \u00b5L 4 units of DNase enzyme and 10 \u00b5L of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37\u00b0C. Phenol 200 \u00b5L and 20 \u00b5L 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 \u00b5L 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 \u00b5L of isopropanol was added to precipitate the RNA. The samples were incubated at  80\u00b0C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 \u00b5L 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 \u00b5L nuclease free water. The RNA was stored at  80\u00b0C. 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 \u22658 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit\u00ae 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\u00ae 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", null, "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, null, null, 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", null, "Ireland", "2019-04-30", "Adult", "Adult", "Multi-tissue", "Multi-system"], [10216, "ERR6501834", "ERX6129007", "ERS7415871", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 3", "SAMEA9691614", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 3 p", "Uninjured 3 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz", "fastq fastq", 18723567013.0, 65061888.0, "E MTAB 10860:un 3 R", "0:143.87 1:143.91", "A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225", 143, 143, null, null, 4417527025, 4932613578, 4960694819, 4412305366, 426225, "ERX6129007", "ERS7415871", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96755, 0.96744, 0.18873, 0.18936, 0.72868, 0.73235, 0.632, 0.6437, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10217, "ERR6501833", "ERX6129006", "ERS7415870", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 2", "SAMEA9691613", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 2 p", "Uninjured 2 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz", "fastq fastq", 16871358399.0, 59064661.0, "E MTAB 10860:un 2 R", "0:142.77 1:142.88", "A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056", 142, 142, null, null, 4041490134, 4380856328, 4414614946, 4033723935, 673056, "ERX6129006", "ERS7415870", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96589, 0.9656, 0.15519, 0.15447, 0.70887, 0.71062, 0.60267, 0.60735, 150, 147, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10218, "ERR6501832", "ERX6129005", "ERS7415869", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 1", "SAMEA9691612", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 1 p", "Uninjured 1 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz", "fastq fastq", 22029484310.0, 76938931.0, "E MTAB 10860:un 1 R", "0:143.11 1:143.22", "A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752", 143, 143, null, null, 5407867825, 5589867496, 5636111894, 5394805343, 831752, "ERX6129005", "ERS7415869", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.9602, 0.95957, 0.14282, 0.14408, 0.69649, 0.69954, 0.56712, 0.56916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10219, "ERR6501831", "ERX6129004", "ERS7415868", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 3", "SAMEA9691611", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 3 p", "Injured 3 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz", "fastq fastq", 7393087749.0, 25640713.0, "E MTAB 10860:in 3 R", "0:144.14 1:144.20", "A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175", 144, 144, null, null, 1776335117, 1913125420, 1928181998, 1775255039, 190175, "ERX6129004", "ERS7415868", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96032, 0.96001, 0.15921, 0.15882, 0.71417, 0.71869, 0.59876, 0.595, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10220, "ERR6501830", "ERX6129003", "ERS7415867", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 2", "SAMEA9691610", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 2 p", "Injured 2 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz", "fastq fastq", 9437508186.0, 33059234.0, "E MTAB 10860:in 2 R", "0:142.70 1:142.77", "A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351", 142, 142, null, null, 2291798254, 2421252733, 2436117818, 2288107030, 232351, "ERX6129003", "ERS7415867", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96099, 0.96042, 0.14616, 0.14802, 0.70331, 0.70674, 0.53288, 0.54459, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10221, "ERR6501829", "ERX6129002", "ERS7415866", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 1", "SAMEA9691609", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 1 p", "Injured 1 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz", "fastq fastq", 15465552702.0, 54194727.0, "E MTAB 10860:in 1 R", "0:142.59 1:142.78", "A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648", 142, 142, null, null, 3807777989, 3911855097, 3946385823, 3798685145, 848648, "ERX6129002", "ERS7415866", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.95721, 0.95688, 0.14331, 0.14374, 0.70262, 0.70445, 0.5114, 0.52855, 140, 140, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [34192, "SRR31443228", "SRX26812023", "SRS23296672", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 3", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 3", "srrm4[y712] mutant replicate 3", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut3.pass2Aligned.sortedByCoord.out.bam", "bam", 23466336192.0, 117587529.0, "25938 mut3.pass2Aligned.sortedByCoord.out.bam", "0:100.13 1:100.08", "A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927", 100, 100, null, null, 6298034402, 5433884683, 5344985734, 6388443446, 987927, "SRX26812023", "SRS23296672", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.95864, 0.95894, 0.10681, 0.1052, 0.65385, 0.65403, 0.46511, 0.46252, 99, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34193, "SRR31443229", "SRX26812022", "SRS23296671", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 3", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 3", "srrm4[y712] wild type replicate 3", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt3.pass2Aligned.sortedByCoord.out.bam", "bam", 23979171134.0, 120156039.0, "25938 wt3.pass2Aligned.sortedByCoord.out.bam", "0:100.12 1:100.07", "A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857", 100, 100, null, null, 6398807397, 5589997524, 5503127729, 6486232627, 1005857, "SRX26812022", "SRS23296671", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.95941, 0.96004, 0.10323, 0.10191, 0.65451, 0.6532, 0.46396, 0.46398, 101, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34194, "SRR31443230", "SRX26812021", "SRS23296670", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 2", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 2", "srrm4[y712] mutant replicate 2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut2.pass2Aligned.sortedByCoord.out.bam", "bam", 20256127500.0, 101792067.0, "25938 mut2.pass2Aligned.sortedByCoord.out.bam", "0:100.05 1:100.00", "A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366", 100, 100, null, null, 5435798119, 4683997479, 4650293108, 5485187428, 851366, "SRX26812021", "SRS23296670", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.96008, 0.96049, 0.10232, 0.10156, 0.66072, 0.65932, 0.4668, 0.46817, 95, 95, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34195, "SRR31443231", "SRX26812020", "SRS23296669", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 2", null, "strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 2", "srrm4[y712] wild type replicate 2", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt2.pass2Aligned.sortedByCoord.out.bam", "bam", 22698373371.0, 113599687.0, "25938 wt2.pass2Aligned.sortedByCoord.out.bam", "0:100.18 1:100.12", "A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128", 100, 100, null, null, 6063922145, 5275724786, 5212055837, 6145709475, 961128, "SRX26812020", "SRS23296669", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.96129, 0.96063, 0.1003, 0.09861, 0.65744, 0.65748, 0.46167, 0.46817, 98, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34196, "SRR31443232", "SRX26812019", "SRS23296667", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] mutant replicate 1", null, "strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] mutant replicate 1", "srrm4[y712] mutant replicate 1", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_mut.pass2Aligned.sortedByCoord.out.bam", "bam", 11282501509.0, 56702666.0, "25938 mut.pass2Aligned.sortedByCoord.out.bam", "0:99.65 1:99.55", "A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849", 99, 99, null, null, 2764745971, 2868447715, 2856237429, 2792914545, 155849, "SRX26812019", "SRS23296667", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [34197, "SRR31443233", "SRX26812018", "SRS23296668", "SRP546978", "PRJNA1189474", "Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf", "PRJNA1189474", "Other", "The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf", null, null, null, null, "srrm4[y712] wild type replicate 1", null, "strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish larvae", "srrm4[y712] wild type replicate 1", "srrm4[y712] wild type replicate 1", "TruSeq library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP546978", null, "assembly:GRCz11", "25938_wt.pass2Aligned.sortedByCoord.out.bam", "bam", 16346812838.0, 82104499.0, "25938 wt.pass2Aligned.sortedByCoord.out.bam", "0:99.65 1:99.56", "A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992", 99, 99, null, null, 3996717287, 4167381503, 4130586142, 4051899914, 227992, "SRX26812018", "SRS23296668", "SRA2019780", "Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology", "Eunice Kennedy Shriver National Institute of Child Health and Human Development", 2, 0.97776, 0.97907, 0.04095, 0.04006, 0.6702, 0.67034, 0.46611, 0.46144, 99, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-22", "Larval", "Larval", "Head", "Nervous System"], [35941, "SRR33299145", "SRX28544240", "SRS24843420", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT4 ppat liver", null, "strain:ppat|isolate:RNA wt4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt4", "RNA wt4", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT4_ppat-liver_S28_R1_001.fastq.gz WT4_ppat-liver_S28_R2_001.fastq.gz", "fastq fastq", 12054556418.0, 60504917.0, "WT4 ppat liver S28 R1 001.fastq.gz", "0:99.62 1:99.61", "A:3156096964;C:2870076825;G:2908548000;T:3118003046;N:1831583", 99, 99, null, null, 3156096964, 2870076825, 2908548000, 3118003046, 1831583, "SRX28544240", "SRS24843420", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35942, "SRR33299146", "SRX28544239", "SRS24843419", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT3 ppat liver", null, "strain:ppat|isolate:RNA wt3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt3", "RNA wt3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT3_ppat-liver_S27_R1_001.fastq.gz WT3_ppat-liver_S27_R2_001.fastq.gz", "fastq fastq", 13917840876.0, 69735355.0, "WT3 ppat liver S27 R1 001.fastq.gz", "0:99.76 1:99.82", "A:3668835621;C:3297107084;G:3353446119;T:3593656283;N:4795769", 99, 99, null, null, 3668835621, 3297107084, 3353446119, 3593656283, 4795769, "SRX28544239", "SRS24843419", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35943, "SRR33299147", "SRX28544238", "SRS24843418", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT2 ppat liver", null, "strain:ppat|isolate:RNA wt2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt2", "RNA wt2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT2_ppat-liver_S26_R1_001.fastq.gz WT2_ppat-liver_S26_R2_001.fastq.gz", "fastq fastq", 13414385259.0, 67138074.0, "WT2 ppat liver S26 R1 001.fastq.gz", "0:99.79 1:100.01", "A:3544883230;C:3160905311;G:3259087045;T:3439671703;N:9837970", 99, 100, null, null, 3544883230, 3160905311, 3259087045, 3439671703, 9837970, "SRX28544238", "SRS24843418", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35944, "SRR33299148", "SRX28544237", "SRS24843417", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT1 ppat liver", null, "strain:ppat|isolate:RNA wt1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt1", "RNA wt1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT1_ppat-liver_S25_R1_001.fastq.gz WT1_ppat-liver_S25_R2_001.fastq.gz", "fastq fastq", 10922184332.0, 54765335.0, "WT1 ppat liver S25 R1 001.fastq.gz", "0:99.61 1:99.82", "A:2868583271;C:2597837660;G:2681619273;T:2767298124;N:6846004", 99, 99, null, null, 2868583271, 2597837660, 2681619273, 2767298124, 6846004, "SRX28544237", "SRS24843417", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35945, "SRR33299149", "SRX28544236", "SRS24843416", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut4 ppat liver", null, "strain:ppat|isolate:RNA mut4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut4", "RNA mut4", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mut4_ppat-liver_S36_R1_001.fastq.gz Mut4_ppat-liver_S36_R2_001.fastq.gz", "fastq fastq", 12530931476.0, 62826169.0, "Mut4 ppat liver S36 R1 001.fastq.gz", "0:99.67 1:99.78", "A:3324393503;C:2939109258;G:3014385499;T:3247670290;N:5372926", 99, 99, null, null, 3324393503, 2939109258, 3014385499, 3247670290, 5372926, "SRX28544236", "SRS24843416", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35946, "SRR33299150", "SRX28544235", "SRS24843415", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut3 ppat liver", null, "strain:ppat|isolate:RNA mut3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut3", "RNA mut3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mut3_ppat-liver_S35_R1_001.fastq.gz Mut3_ppat-liver_S35_R2_001.fastq.gz", "fastq fastq", 10720402854.0, 53894468.0, "Mut3 ppat liver S35 R1 001.fastq.gz", "0:99.40 1:99.52", "A:2864014346;C:2503521968;G:2584948225;T:2763732849;N:4185466", 99, 99, null, null, 2864014346, 2503521968, 2584948225, 2763732849, 4185466, "SRX28544235", "SRS24843415", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35947, "SRR33299151", "SRX28544234", "SRS24843414", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut2 ppat liver", null, "strain:ppat|isolate:RNA mut2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut2", "RNA mut2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mut2_ppat-liver_S34_R1_001.fastq.gz Mut2_ppat-liver_S34_R2_001.fastq.gz", "fastq fastq", 13658984938.0, 68656301.0, "Mut2 ppat liver S34 R1 001.fastq.gz", "0:99.35 1:99.59", "A:3634178483;C:3189694846;G:3300982525;T:3525339026;N:8790058", 99, 99, null, null, 3634178483, 3189694846, 3300982525, 3525339026, 8790058, "SRX28544234", "SRS24843414", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35948, "SRR33299152", "SRX28544233", "SRS24843413", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut1 ppat liver", null, "strain:ppat|isolate:RNA mut1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut1", "RNA mut1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mut1_ppat-liver_S33_R1_001.fastq.gz Mut1_ppat-liver_S33_R2_001.fastq.gz", "fastq fastq", 10934728288.0, 54995591.0, "Mut1 ppat liver S33 R1 001.fastq.gz", "0:99.36 1:99.47", "A:2909267644;C:2564520996;G:2638675283;T:2818803981;N:3460384", 99, 99, null, null, 2909267644, 2564520996, 2638675283, 2818803981, 3460384, "SRX28544233", "SRS24843413", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35949, "SRR33299154", "SRX28544231", "SRS24843411", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Het4 ppat liver", null, "strain:ppat|isolate:RNA het4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA het4", "RNA het4", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Het4_ppat-liver_S32_R1_001.fastq.gz Het4_ppat-liver_S32_R2_001.fastq.gz", "fastq fastq", 11933665535.0, 59956025.0, "Het4 ppat liver S32 R1 001.fastq.gz", "0:99.47 1:99.57", "A:3167338389;C:2796677179;G:2888967002;T:3076290728;N:4392237", 99, 99, null, null, 3167338389, 2796677179, 2888967002, 3076290728, 4392237, "SRX28544231", "SRS24843411", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35950, "SRR33299155", "SRX28544230", "SRS24843410", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Het3 ppat liver", null, "strain:ppat|isolate:RNA het3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA het3", "RNA het3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Het3_ppat-liver_S31_R1_001.fastq.gz Het3_ppat-liver_S31_R2_001.fastq.gz", "fastq fastq", 8736836848.0, 43909775.0, "Het3 ppat liver S31 R1 001.fastq.gz", "0:99.49 1:99.48", "A:2316148154;C:2054859781;G:2098968973;T:2265744694;N:1115246", 99, 99, null, null, 2316148154, 2054859781, 2098968973, 2265744694, 1115246, "SRX28544230", "SRS24843410", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35951, "SRR33299156", "SRX28544229", "SRS24843409", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Het2 ppat liver", null, "strain:ppat|isolate:RNA het2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA het2", "RNA het2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Het2_ppat-liver_S30_R1_001.fastq.gz Het2_ppat-liver_S30_R2_001.fastq.gz", "fastq fastq", 7931230506.0, 39763891.0, "Het2 ppat liver S30 R1 001.fastq.gz", "0:99.72 1:99.74", "A:2118901869;C:1861115765;G:1903240420;T:2046832152;N:1140300", 99, 99, null, null, 2118901869, 1861115765, 1903240420, 2046832152, 1140300, "SRX28544229", "SRS24843409", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35952, "SRR33299157", "SRX28544228", "SRS24843408", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Het1 ppat liver", null, "strain:ppat|isolate:RNA het1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA het1", "RNA het1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Het1_ppat-liver_S29_R1_001.fastq.gz Het1_ppat-liver_S29_R2_001.fastq.gz", "fastq fastq", 8695997521.0, 43696765.0, "Het1 ppat liver S29 R1 001.fastq.gz", "0:99.39 1:99.62", "A:2300583830;C:2047586482;G:2114382364;T:2227671389;N:5773456", 99, 99, null, null, 2300583830, 2047586482, 2114382364, 2227671389, 5773456, "SRX28544228", "SRS24843408", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Adult", "Adult", "Liver", "Liver and Biliary System"], [35953, "SRR33299171", "SRX28544214", "SRS24843394", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT pos 3", null, "strain:ppat|isolate:RNA wt pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt pos 3", "RNA wt pos 3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-pos-3_S10_R1_001.fastq.gz WT-pos-3_S10_R2_001.fastq.gz", "fastq fastq", 15038194818.0, 74446509.0, "WT pos 3 S10 R1 001.fastq.gz", "0:101 1:101", "A:4616878123;C:2865206674;G:2927449871;T:4628427327;N:232823", 101, 101, null, null, 4616878123, 2865206674, 2927449871, 4628427327, 232823, "SRX28544214", "SRS24843394", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35954, "SRR33299172", "SRX28544213", "SRS24843393", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT pos 2", null, "strain:ppat|isolate:RNA wt pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt pos 2", "RNA wt pos 2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-pos-2_S6_R1_001.fastq.gz WT-pos-2_S6_R2_001.fastq.gz", "fastq fastq", 12522438742.0, 61992271.0, "WT pos 2 S6 R1 001.fastq.gz", "0:101 1:101", "A:3774656054;C:2451528285;G:2501043573;T:3795016419;N:194411", 101, 101, null, null, 3774656054, 2451528285, 2501043573, 3795016419, 194411, "SRX28544213", "SRS24843393", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35955, "SRR33299173", "SRX28544212", "SRS24843392", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. 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Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. 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Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. 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Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. 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Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies  but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development  gametogenesis  and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants  identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. 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[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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"technology\" = :p2 order by rowid limit 101", "params": {"p0": "PAIRED", "p1": "PolyA", "p2": "bulk"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", 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"column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk", "results": [{"value": "Larval", "label": "Larval", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&devstage_curation_coarse=Larval", "selected": false}, {"value": "Adult", "label": "Adult", 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{"value": "Adult", "label": "Adult", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&devstage_curation=Adult", "selected": false}, {"value": "Hatching", "label": "Hatching", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&devstage_curation=Hatching", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk", "results": [{"value": "Liver and Biliary System", "label": "Liver and Biliary System", "count": 24, "toggle_url": 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"/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk", "results": [{"value": "Liver", "label": "Liver", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&tissue_curation=Liver", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&tissue_curation=Undetermined", "selected": false}, {"value": "Head", "label": "Head", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=PAIRED&experiment.library_selection=PolyA&technology=bulk&tissue_curation=Head", "selected": false}, {"value": "Heart", "label": "Heart", "count": 6, "toggle_url": 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