{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\" 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"], [10391, "ERR8516975", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R", "0:51 1:51", "A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852", 51, 51, null, null, 1077092958, 949537387, 955020348, 1099432979, 20556852, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.9053, 0.9259, 0.21658, 0.22155, 0.69369, 0.69179, 0.50726, 0.50871, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10392, "ERR8516976", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R", "0:51 1:51", "A:972081222;C:890179393;G:888655698;T:998443264;N:18934747", 51, 51, null, null, 972081222, 890179393, 888655698, 998443264, 18934747, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.86107, 0.87807, 0.22063, 0.23029, 0.70859, 0.70561, 0.51656, 0.51946, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10393, "ERR8516977", "ERX8083451", "ERS10521298", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling neurite", "SAMEA12922152", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling neurite p", "Sibling neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R", "0:51 1:51", "A:728798881;C:962223604;G:958876331;T:735449513;N:17094231", 51, 51, null, null, 728798881, 962223604, 958876331, 735449513, 17094231, "ERX8083451", "ERS10521298", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.54616, 0.55881, 0.13313, 0.14036, 0.84295, 0.84185, 0.64193, 0.59762, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10394, "ERR8516972", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R", "0:51 1:51", "A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786", 51, 51, null, null, 837274632, 1062368015, 1049892288, 853310517, 19213786, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.5726, 0.57788, 0.13781, 0.14082, 0.80616, 0.80452, 0.61581, 0.60389, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10395, "ERR8516973", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R", "0:51 1:51", "A:897813231;C:796012893;G:794839496;T:923696030;N:17221274", 51, 51, null, null, 897813231, 796012893, 794839496, 923696030, 17221274, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.92095, 0.94156, 0.18892, 0.20024, 0.6901, 0.68905, 0.49377, 0.50086, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10396, "ERR8516974", "ERX8083450", "ERS10521297", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Sibling cellular", "SAMEA12922151", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Sibling cellular p", "Sibling cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R", "0:51 1:51", "A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248", 51, 51, null, null, 951912827, 1107150666, 1086060798, 973791571, 20785248, "ERX8083450", "ERS10521297", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.63792, 0.62667, 0.18547, 0.18671, 0.78756, 0.78549, 0.59274, 0.55478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10397, "ERR8516969", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R", "0:51 1:51", "A:925784769;C:934445856;G:959155668;T:924080408;N:18878983", 51, 51, null, null, 925784769, 934445856, 959155668, 924080408, 18878983, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.59503, 0.61112, 0.1947, 0.20225, 0.76512, 0.76337, 0.54584, 0.54345, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10398, "ERR8516970", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R", "0:51 1:51", "A:991755033;C:864808531;G:892202564;T:992188806;N:18881958", 51, 51, null, null, 991755033, 864808531, 892202564, 992188806, 18881958, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.86612, 0.88689, 0.26181, 0.2728, 0.7094, 0.7091, 0.53639, 0.53906, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10399, "ERR8516971", "ERX8083449", "ERS10521296", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null neurite", "SAMEA12922150", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null neurite p", "Null neurite p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neurite", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R", "0:51 1:51", "A:766707527;C:798667604;G:818782599;T:773280942;N:15938306", 51, 51, null, null, 766707527, 798667604, 818782599, 773280942, 15938306, "ERX8083449", "ERS10521296", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.88811, 0.92834, 0.21869, 0.22669, 0.72878, 0.72604, 0.55598, 0.57831, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10400, "ERR8516966", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R", "0:51 1:51", "A:774360373;C:720215184;G:719479745;T:796239200;N:15182374", 51, 51, null, null, 774360373, 720215184, 719479745, 796239200, 15182374, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.79643, 0.81194, 0.25554, 0.2603, 0.72236, 0.72021, 0.51775, 0.51678, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10401, "ERR8516967", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R", "0:51 1:51", "A:739921027;C:667375549;G:663864111;T:764302396;N:14288091", 51, 51, null, null, 739921027, 667375549, 663864111, 764302396, 14288091, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.90817, 0.92909, 0.23387, 0.24814, 0.70088, 0.69842, 0.51238, 0.51267, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [10402, "ERR8516968", "ERX8083448", "ERS10521295", "ERP135383", "PRJEB50776", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E-MTAB-11431", "Other", "Zebrafish primary neurons either sfpq sibling/control +/+  +/  or null  /  were cultured in transwell inserts. At DIV2  for each genotype  cellular and neurite tissues were separately isolated  RNA extracted and total RNAseq performed.", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19", null, "Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Null cellular", "SAMEA12922149", "Centre for Developmental Neurobiology, King's College London", "ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology  King's College London|INSDC center name:Centre for Developmental Neurobiology  King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null  / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "E MTAB 11431:Null cellular p", "Null cellular p", "Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing  and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion", "Experimental Factor: genotype:sfpq null  / |Experimental Factor: organism part:neuron", "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP135383", "Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+  +/  and null  /  primary zebrafish neuron cellular and neurite tissue", "ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py", "15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz", "fastq fastq", null, null, "E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R", "0:51 1:51", "A:882831441;C:935213418;G:957033335;T:879085993;N:18444957", 51, 51, null, null, 882831441, 935213418, 957033335, 879085993, 18444957, "ERX8083448", "ERS10521295", "ERA8932807", "Centre for Developmental Neurobiology, King", "Centre for Developmental Neurobiology, King", 2, 0.76218, 0.7682, 0.18357, 0.18521, 0.74444, 0.74272, 0.46714, 0.55518, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-02-19", "Undetermined", "Undetermined", "Brain", "Nervous System"], [11226, "ERR10368639", "ERX9900562", "ERS13563108", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X9", "SAMEA111469072", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469072|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X9|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70  / |organism part:whole organism|sample name:E MTAB 12301:16261X9", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X9 p", "16261X9 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:snrnp70  / ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R1_001.fastq.gz 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R2_001.fastq.gz", "fastq fastq", 2686590240.0, 26339120.0, "E MTAB 12301:16261X9 190815 A00421 0101 BHFL23DRXX S2 L001 R", "0:51 1:51", "A:694597606;C:635153638;G:628248232;T:728333026;N:257738", 51, 51, null, null, 694597606, 635153638, 628248232, 728333026, 257738, "ERX9900562", "ERS13563108", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94614, 0.94723, 0.1538, 0.15109, 0.70398, 0.70352, 0.48123, 0.48168, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11227, "ERR10368638", "ERX9900561", "ERS13563107", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X8", "SAMEA111469071", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469071|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X8|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70  / |organism part:whole organism|sample name:E MTAB 12301:16261X8", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X8 p", "16261X8 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:snrnp70  / ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R1_001.fastq.gz 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R2_001.fastq.gz", "fastq fastq", 15003930006.0, 147097353.0, "E MTAB 12301:16261X8 190815 A00421 0101 BHFL23DRXX S4 L001 R", "0:51 1:51", "A:3882939949;C:3570150556;G:3520942177;T:4028462946;N:1434378", 51, 51, null, null, 3882939949, 3570150556, 3520942177, 4028462946, 1434378, "ERX9900561", "ERS13563107", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94373, 0.94762, 0.17954, 0.17832, 0.70299, 0.70207, 0.48822, 0.48842, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11228, "ERR10368637", "ERX9900560", "ERS13563106", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X7", "SAMEA111469070", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469070|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X7|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70  / |organism part:whole organism|sample name:E MTAB 12301:16261X7", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X7 p", "16261X7 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:snrnp70  / ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py", "16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R1_001.fastq.gz 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R2_001.fastq.gz", "fastq fastq", 3806643060.0, 37320030.0, "E MTAB 12301:16261X7 190815 A00421 0101 BHFL23DRXX S6 L001 R", "0:51 1:51", "A:971582421;C:919313664;G:905728446;T:1009653865;N:364664", 51, 51, null, null, 971582421, 919313664, 905728446, 1009653865, 364664, "ERX9900560", "ERS13563106", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94035, 0.94356, 0.1661, 0.16393, 0.70136, 0.70082, 0.48294, 0.48049, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11229, "ERR10368636", "ERX9900559", "ERS13563105", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X6", "SAMEA111469069", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469069|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X6|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X6", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X6 p", "16261X6 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:+/cyt hSNRNP70", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R1_001.fastq.gz 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R2_001.fastq.gz", "fastq fastq", 2875874598.0, 28194849.0, "E MTAB 12301:16261X6 190815 A00421 0101 BHFL23DRXX S7 L001 R", "0:51 1:51", "A:745870043;C:683782229;G:673037324;T:772909720;N:275282", 51, 51, null, null, 745870043, 683782229, 673037324, 772909720, 275282, "ERX9900559", "ERS13563105", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.9435, 0.94737, 0.16987, 0.16888, 0.6983, 0.69826, 0.47122, 0.47409, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11230, "ERR10368635", "ERX9900558", "ERS13563104", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X5", "SAMEA111469068", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469068|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X5|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X5", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X5 p", "16261X5 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:+/cyt hSNRNP70", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R1_001.fastq.gz 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R2_001.fastq.gz", "fastq fastq", 2656716072.0, 26046236.0, "E MTAB 12301:16261X5 190815 A00421 0101 BHFL23DRXX S8 L001 R", "0:51 1:51", "A:693979046;C:627484571;G:617505105;T:717493108;N:254242", 51, 51, null, null, 693979046, 627484571, 617505105, 717493108, 254242, "ERX9900558", "ERS13563104", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94387, 0.94796, 0.16299, 0.16183, 0.69556, 0.69581, 0.46842, 0.47334, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11231, "ERR10368634", "ERX9900557", "ERS13563103", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X4", "SAMEA111469067", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469067|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X4|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X4", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X4 p", "16261X4 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:+/cyt hSNRNP70", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R1_001.fastq.gz 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R2_001.fastq.gz", "fastq fastq", 2693177298.0, 26403699.0, "E MTAB 12301:16261X4 190815 A00421 0101 BHFL23DRXX S9 L001 R", "0:51 1:51", "A:698547378;C:640687214;G:628869192;T:724816757;N:256757", 51, 51, null, null, 698547378, 640687214, 628869192, 724816757, 256757, "ERX9900557", "ERS13563103", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94101, 0.94526, 0.17344, 0.17201, 0.68619, 0.68513, 0.47366, 0.4702, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11232, "ERR10368633", "ERX9900556", "ERS13563102", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X3", "SAMEA111469066", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469066|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X3|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X3", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X3 p", "16261X3 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py|options:  dnus", "16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R1_001.fastq.gz 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R2_001.fastq.gz", "fastq fastq", 3104796462.0, 60878362.0, "E MTAB 12301:16261X3 190815 A00421 0101 BHFL23DRXX S10 L001 R", "0:51", "A:803595677;C:737898133;G:731641815;T:831364716;N:296121", 51, null, null, null, 803595677, 737898133, 731641815, 831364716, 296121, "ERX9900556", "ERS13563102", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 1, 0.94361, null, 0.16161, null, 0.69822, null, 0.4647, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11233, "ERR10368632", "ERX9900555", "ERS13563101", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X2", "SAMEA111469065", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469065|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X2|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X2", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X2 p", "16261X2 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R1_001.fastq.gz 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R2_001.fastq.gz", "fastq fastq", 2935625892.0, 28780646.0, "E MTAB 12301:16261X2 190815 A00421 0101 BHFL23DRXX S11 L001 R", "0:51 1:51", "A:759844700;C:699591057;G:694530268;T:781380766;N:279101", 51, 51, null, null, 759844700, 699591057, 694530268, 781380766, 279101, "ERX9900555", "ERS13563101", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.93297, 0.93744, 0.16748, 0.16566, 0.69929, 0.6996, 0.4788, 0.47875, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11234, "ERR10368631", "ERX9900554", "ERS13563100", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X12", "SAMEA111469064", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469064|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X12|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X12", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X12 p", "16261X12 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:cyt hSNRNP70/ ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R1_001.fastq.gz 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R2_001.fastq.gz", "fastq fastq", 7451469240.0, 73053620.0, "E MTAB 12301:16261X12 190815 A00421 0101 BHFL23DRXX S3 L001 R", "0:51 1:51", "A:1950856364;C:1747213644;G:1718730947;T:2033957057;N:711228", 51, 51, null, null, 1950856364, 1747213644, 1718730947, 2033957057, 711228, "ERX9900554", "ERS13563100", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.9372, 0.94118, 0.20267, 0.19972, 0.69794, 0.69735, 0.47505, 0.4883, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11235, "ERR10368630", "ERX9900553", "ERS13563099", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X11", "SAMEA111469063", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469063|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X11|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X11", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X11 p", "16261X11 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:cyt hSNRNP70/ ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", "16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R1_001.fastq.gz 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R2_001.fastq.gz", "fastq fastq", 2754589458.0, 27005779.0, "E MTAB 12301:16261X11 190815 A00421 0101 BHFL23DRXX S5 L001 R", "0:51 1:51", "A:715675810;C:652231961;G:640938288;T:745480460;N:262939", 51, 51, null, null, 715675810, 652231961, 640938288, 745480460, 262939, "ERX9900553", "ERS13563099", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.93802, 0.94247, 0.17937, 0.17728, 0.70195, 0.70067, 0.48458, 0.48364, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11236, "ERR10368629", "ERX9900552", "ERS13563098", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X10", "SAMEA111469062", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469062|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X10|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X10", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X10 p", "16261X10 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:cyt hSNRNP70/ ", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py", "16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R1_001.fastq.gz 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R2_001.fastq.gz", "fastq fastq", 2319764682.0, 22742791.0, "E MTAB 12301:16261X10 190815 A00421 0101 BHFL23DRXX S1 L001 R", "0:51 1:51", "A:596937200;C:555502273;G:546190804;T:620912915;N:221490", 51, 51, null, null, 596937200, 555502273, 546190804, 620912915, 221490, "ERX9900552", "ERS13563098", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94034, 0.94451, 0.1621, 0.16043, 0.69406, 0.6928, 0.4936, 0.49757, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11237, "ERR10368628", "ERX9900551", "ERS13563097", "ERP141667", "PRJEB56699", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E-MTAB-12301", "Other", "It has been recently shown that SNRNP70  a major component of the spliceosome  as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons  we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein  we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that  we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling  ii siblings/cyt hSNRNP70  iii null  iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced.", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31", null, "Protocols: Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "16261X1", "SAMEA111469061", "Department of Life Sciences University of Bath", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469061|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X1|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X1", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "E MTAB 12301:16261X1 p", "16261X1 p", "RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "Embryos were collected and raised in Danieau's solution together with 2 \u03bc\u039c 4 OH\u03a4. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP141667", "Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70", "ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py", "16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R1_001.fastq.gz 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R2_001.fastq.gz", "fastq fastq", 2992675512.0, 29339956.0, "E MTAB 12301:16261X1 190815 A00421 0101 BHFL23DRXX S12 L001 R", "0:51 1:51", "A:768607745;C:718646844;G:713246748;T:791888447;N:285728", 51, 51, null, null, 768607745, 718646844, 713246748, 791888447, 285728, "ERX9900551", "ERS13563097", "ERA18523376", "Department of Life Sciences University of Bath|European Nucleotide Archive", "Department of Life Sciences University of Bath|European Nucleotide Archive", 2, 0.94414, 0.94881, 0.16725, 0.16648, 0.68909, 0.68923, 0.47873, 0.48244, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "trueseq", "bulk", "bulk", "bulk", null, "United Kingdom", "2022-10-31", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [11815, "ERR11799086", "ERX11197445", "ERS16222830", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 4", "SAMEA114237385", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 4 p", "Sample 4 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz", "fastq fastq", 19305011730.0, 95569365.0, "E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R", "0:101 1:101", "A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044", 101, 101, null, null, 6768262250, 3044091042, 2847188942, 6645295452, 174044, "ERX11197445", "ERS16222830", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.57007, 0.5231, 0.45597, 0.40582, 0.91579, 0.91674, 0.58257, 0.5625, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [11816, "ERR11799088", "ERX11197447", "ERS16222832", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 6", "SAMEA114237387", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237387|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 6|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 6|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 6 p", "Sample 6 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz", "fastq fastq", 21028230098.0, 104100149.0, "E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R", "0:101 1:101", "A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043", 101, 101, null, null, 6738894716, 4007335499, 3664578692, 6617229148, 192043, "ERX11197447", "ERS16222832", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.69217, 0.69414, 0.45934, 0.4539, 0.86423, 0.86344, 0.64485, 0.62976, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [11817, "ERR11799085", "ERX11197444", "ERS16222829", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 3", "SAMEA114237384", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237384|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 3|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 3|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 3 p", "Sample 3 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz", "fastq fastq", 20720724286.0, 102577843.0, "E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R", "0:101 1:101", "A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303", 101, 101, null, null, 7221245295, 3305546836, 3154595537, 7039147315, 189303, "ERX11197444", "ERS16222829", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.6027, 0.56103, 0.46397, 0.41738, 0.90536, 0.90473, 0.59858, 0.59246, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [11818, "ERR11799087", "ERX11197446", "ERS16222831", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 5", "SAMEA114237386", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237386|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 5|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 5|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 5 p", "Sample 5 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz", "fastq fastq", 20557799368.0, 101771284.0, "E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R", "0:101 1:101", "A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476", 101, 101, null, null, 5872430236, 4635392917, 4244261404, 5805533335, 181476, "ERX11197446", "ERS16222831", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.48524, 0.49426, 0.30765, 0.31318, 0.87008, 0.86918, 0.60597, 0.58678, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [11819, "ERR11799083", "ERX11197442", "ERS16222827", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 1", "SAMEA114237382", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237382|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 1|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 1 p", "Sample 1 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz", "fastq fastq", 24592452226.0, 121744813.0, "E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R", "0:101 1:101", "A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659", 101, 101, null, null, 6964719283, 5587681189, 5075783189, 6964040906, 227659, "ERX11197442", "ERS16222827", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.82038, 0.82668, 0.39096, 0.39605, 0.82532, 0.82446, 0.63514, 0.57014, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [11820, "ERR11799084", "ERX11197443", "ERS16222828", "ERP149963", "PRJEB64798", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E-MTAB-13228", "Transcriptome Analysis", "We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish  allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells  respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter  and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", "Sample 2", "SAMEA114237383", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237383|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 2|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 2|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "E MTAB 13228:Sample 2 p", "Sample 2 p", "Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low  n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high  n=2 were sorted.  RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set", null, "RNA-Seq", "TRANSCRIPTOMIC", "Inverse rRNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP149963", "Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz", "fastq fastq", 23692841994.0, 117291297.0, "E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R", "0:101 1:101", "A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078", 101, 101, null, null, 6997658831, 5103576511, 4615471075, 6975924499, 211078, "ERX11197443", "ERS16222828", "ERA26360556", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.78961, 0.79279, 0.39456, 0.39476, 0.8227, 0.82309, 0.62072, 0.61776, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [15028, "ERR594449", "ERX552402", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 010", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_010_R1.fastq.gz McGrail_PT_MM02_010_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 010 R", "0:100 1:100", "A:871527648;C:730105705;G:727172263;T:866698092;N:4496292", 100, 100, null, null, 871527648, 730105705, 727172263, 866698092, 4496292, "ERX552402", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92177, 0.92501, 0.1237, 0.1262, 0.69844, 0.7009, 0.49781, 0.4982, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15029, "ERR594457", "ERX552401", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 002", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_002_R1.fastq.gz McGrail_PT_MM02_002_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 002 R", "0:100 1:100", "A:872387737;C:732112926;G:726274702;T:868026782;N:1197853", 100, 100, null, null, 872387737, 732112926, 726274702, 868026782, 1197853, "ERX552401", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92719, 0.92684, 0.126, 0.12696, 0.69684, 0.70118, 0.49645, 0.50037, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15030, "ERR594456", "ERX552400", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 004", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_004_R2.fastq.gz McGrail_T_MM01_004_R1.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 004 R", "0:100 1:100", "A:849885320;C:752565271;G:741295555;T:853272249;N:2981605", 100, 100, null, null, 849885320, 752565271, 741295555, 853272249, 2981605, "ERX552400", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93431, 0.93209, 0.09121, 0.09114, 0.67842, 0.68065, 0.49543, 0.48591, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15031, "ERR594431", "ERX552399", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 014", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_014_R1.fastq.gz MM03_WT_L003_014_R2.fastq.gz", "fastq fastq", 2051137800.0, 10255689.0, "E MTAB 2886:MM03 WT L003 014 R", "0:100 1:100", "A:574425675;C:454197762;G:448836898;T:573386204;N:291261", 100, 100, null, null, 574425675, 454197762, 448836898, 573386204, 291261, "ERX552399", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91659, 0.91612, 0.14679, 0.14915, 0.7163, 0.72188, 0.49275, 0.49876, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15032, "ERR594437", "ERX552398", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 006", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_006_R1.fastq.gz MM03_WT_L003_006_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 006 R", "0:100 1:100", "A:892528148;C:712696530;G:702466589;T:891189817;N:1118916", 100, 100, null, null, 892528148, 712696530, 702466589, 891189817, 1118916, "ERX552398", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91798, 0.9161, 0.14538, 0.14613, 0.71401, 0.71656, 0.48443, 0.48666, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15033, "ERR594420", "ERX552397", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 014", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_014_R1.fastq.gz McGrail_PT_MM02_014_R2.fastq.gz", "fastq fastq", 2883852800.0, 14419264.0, "E MTAB 2886:McGrail PT MM02 014 R", "0:100 1:100", "A:787372572;C:658074713;G:654251401;T:783994205;N:159909", 100, 100, null, null, 787372572, 658074713, 654251401, 783994205, 159909, "ERX552397", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92417, 0.9255, 0.12479, 0.12619, 0.69942, 0.7035, 0.50149, 0.49379, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15034, "ERR594450", "ERX552396", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 014", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_014_R1.fastq.gz McGrail_T_MM01_014_R2.fastq.gz", "fastq fastq", 632445400.0, 3162227.0, "E MTAB 2886:McGrail T MM01 014 R", "0:100 1:100", "A:168708082;C:147923885;G:146292680;T:169438791;N:81962", 100, 100, null, null, 168708082, 147923885, 146292680, 169438791, 81962, "ERX552396", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93335, 0.93318, 0.09287, 0.09485, 0.68205, 0.68846, 0.4841, 0.49015, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15035, "ERR594453", "ERX552395", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 011", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_011_R1.fastq.gz McGrail_T_MM01_011_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 011 R", "0:100 1:100", "A:852133250;C:751414688;G:741468348;T:854136333;N:847381", 100, 100, null, null, 852133250, 751414688, 741468348, 854136333, 847381, "ERX552395", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93354, 0.93309, 0.09259, 0.09299, 0.68085, 0.68347, 0.48686, 0.48742, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15036, "ERR594429", "ERX552394", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 002", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_002_R1.fastq.gz McGrail_T_MM01_002_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 002 R", "0:100 1:100", "A:851061858;C:752624348;G:741241133;T:854588994;N:483667", 100, 100, null, null, 851061858, 752624348, 741241133, 854588994, 483667, "ERX552394", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.9341, 0.93285, 0.09214, 0.09303, 0.68036, 0.68465, 0.4888, 0.4918, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15037, "ERR594444", "ERX552393", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 007", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_007_R1.fastq.gz McGrail_PT_MM02_007_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 007 R", "0:100 1:100", "A:871235248;C:733455837;G:726280934;T:868628388;N:399593", 100, 100, null, null, 871235248, 733455837, 726280934, 868628388, 399593, "ERX552393", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92587, 0.9237, 0.12434, 0.12596, 0.69729, 0.70473, 0.49751, 0.49568, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15038, "ERR594436", "ERX552392", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 010", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_010_R1.fastq.gz MM03_WT_L003_010_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 010 R", "0:100 1:100", "A:893317570;C:712391457;G:703064824;T:890653459;N:572690", 100, 100, null, null, 893317570, 712391457, 703064824, 890653459, 572690, "ERX552392", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91775, 0.91713, 0.14296, 0.14486, 0.7136, 0.71638, 0.50074, 0.49246, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15039, "ERR594454", "ERX552391", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 003", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_003_R1.fastq.gz MM03_WT_L003_003_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 003 R", "0:100 1:100", "A:891513936;C:713529681;G:702140879;T:891351829;N:1463675", 100, 100, null, null, 891513936, 713529681, 702140879, 891351829, 1463675, "ERX552391", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91714, 0.91621, 0.14364, 0.14479, 0.71384, 0.71967, 0.48172, 0.4892, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15040, "ERR594422", "ERX552378", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 001", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_001_R1.fastq.gz McGrail_T_MM01_001_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 001 R", "0:100 1:100", "A:849397709;C:754334352;G:741772141;T:853832972;N:662826", 100, 100, null, null, 849397709, 754334352, 741772141, 853832972, 662826, "ERX552378", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93478, 0.93297, 0.09219, 0.09261, 0.67949, 0.68205, 0.48892, 0.47759, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15041, "ERR594433", "ERX552377", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 009", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_009_R1.fastq.gz MM03_WT_L003_009_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 009 R", "0:100 1:100", "A:895908752;C:709459693;G:701325342;T:892915017;N:391196", 100, 100, null, null, 895908752, 709459693, 701325342, 892915017, 391196, "ERX552377", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91776, 0.91744, 0.14402, 0.14626, 0.71435, 0.71794, 0.48624, 0.49768, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15042, "ERR594419", "ERX552376", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 011", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_011_R1.fastq.gz MM03_WT_L003_011_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 011 R", "0:100 1:100", "A:894536120;C:711072714;G:702055612;T:891872676;N:462878", 100, 100, null, null, 894536120, 711072714, 702055612, 891872676, 462878, "ERX552376", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91628, 0.91598, 0.14427, 0.14587, 0.71293, 0.71575, 0.48688, 0.49317, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15043, "ERR594447", "ERX552375", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 004", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_004_R1.fastq.gz MM03_WT_L003_004_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 004 R", "0:100 1:100", "A:893087129;C:711953975;G:702111417;T:891168240;N:1679239", 100, 100, null, null, 893087129, 711953975, 702111417, 891168240, 1679239, "ERX552375", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91793, 0.91708, 0.14418, 0.1457, 0.71052, 0.71405, 0.50617, 0.49339, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15044, "ERR594441", "ERX552374", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 004", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_004_R1.fastq.gz McGrail_PT_MM02_004_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 004 R", "0:100 1:100", "A:869694755;C:734631291;G:727458512;T:866857422;N:1358020", 100, 100, null, null, 869694755, 734631291, 727458512, 866857422, 1358020, "ERX552374", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92607, 0.9248, 0.12414, 0.12446, 0.69686, 0.6995, 0.50202, 0.50333, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15045, "ERR594455", "ERX552373", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 002", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_002_R1.fastq.gz MM03_WT_L003_002_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 002 R", "0:100 1:100", "A:894222634;C:711188537;G:702167816;T:891816353;N:604660", 100, 100, null, null, 894222634, 711188537, 702167816, 891816353, 604660, "ERX552373", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.9174, 0.91577, 0.14516, 0.14534, 0.71342, 0.71756, 0.48084, 0.50033, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15046, "ERR594439", "ERX552410", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 007", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_007_R1.fastq.gz McGrail_T_MM01_007_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 007 R", "0:100 1:100", "A:850777874;C:752786693;G:741650641;T:854268527;N:516265", 100, 100, null, null, 850777874, 752786693, 741650641, 854268527, 516265, "ERX552410", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93398, 0.93264, 0.0917, 0.09232, 0.67878, 0.68172, 0.48311, 0.48417, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15047, "ERR594426", "ERX552409", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 012", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_012_R1.fastq.gz McGrail_T_MM01_012_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 012 R", "0:100 1:100", "A:851190790;C:752415289;G:742719596;T:852979263;N:695062", 100, 100, null, null, 851190790, 752415289, 742719596, 852979263, 695062, "ERX552409", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93297, 0.9327, 0.09093, 0.09105, 0.68043, 0.68282, 0.48563, 0.48327, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15048, "ERR594417", "ERX552390", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 007", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_007_R1.fastq.gz MM03_WT_L003_007_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 007 R", "0:100 1:100", "A:893566548;C:711756657;G:701577232;T:892509486;N:590077", 100, 100, null, null, 893566548, 711756657, 701577232, 892509486, 590077, "ERX552390", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.9176, 0.91644, 0.14542, 0.14641, 0.71358, 0.71713, 0.48742, 0.50207, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15049, "ERR594418", "ERX552389", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 008", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_008_R1.fastq.gz McGrail_T_MM01_008_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 008 R", "0:100 1:100", "A:851314323;C:752411525;G:742349039;T:853577153;N:347960", 100, 100, null, null, 851314323, 752411525, 742349039, 853577153, 347960, "ERX552389", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93343, 0.93187, 0.09175, 0.09249, 0.68016, 0.68164, 0.47952, 0.48824, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15050, "ERR594440", "ERX552388", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 013", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_013_R1.fastq.gz McGrail_T_MM01_013_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 013 R", "0:100 1:100", "A:852425880;C:750595968;G:742140159;T:854286637;N:551356", 100, 100, null, null, 852425880, 750595968, 742140159, 854286637, 551356, "ERX552388", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93231, 0.93338, 0.09134, 0.09313, 0.67945, 0.68256, 0.48693, 0.48084, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15051, "ERR594430", "ERX552387", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 006", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_006_R1.fastq.gz McGrail_PT_MM02_006_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 006 R", "0:100 1:100", "A:869575312;C:734964855;G:727824124;T:866586174;N:1049535", 100, 100, null, null, 869575312, 734964855, 727824124, 866586174, 1049535, "ERX552387", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.9265, 0.92348, 0.12368, 0.12345, 0.69818, 0.70017, 0.4966, 0.50082, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15052, "ERR594445", "ERX552386", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 012", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_012_R1.fastq.gz McGrail_PT_MM02_012_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 012 R", "0:100 1:100", "A:870939166;C:729921300;G:724359208;T:865762186;N:9018140", 100, 100, null, null, 870939166, 729921300, 724359208, 865762186, 9018140, "ERX552386", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92143, 0.92467, 0.1229, 0.12533, 0.69828, 0.70015, 0.50049, 0.4981, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15053, "ERR594434", "ERX552385", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 013", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_013_R1.fastq.gz MM03_WT_L003_013_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 013 R", "0:100 1:100", "A:894614606;C:711109946;G:702301073;T:891485450;N:488925", 100, 100, null, null, 894614606, 711109946, 702301073, 891485450, 488925, "ERX552385", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91697, 0.91671, 0.1447, 0.14584, 0.71327, 0.7176, 0.48116, 0.49462, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15054, "ERR594443", "ERX552372", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 011", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_011_R1.fastq.gz McGrail_PT_MM02_011_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 011 R", "0:100 1:100", "A:869080240;C:728959737;G:723451216;T:862492567;N:16016240", 100, 100, null, null, 869080240, 728959737, 723451216, 862492567, 16016240, "ERX552372", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91732, 0.92471, 0.12164, 0.12427, 0.69739, 0.69773, 0.50246, 0.50104, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15055, "ERR594425", "ERX552371", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 003", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_003_R1.fastq.gz McGrail_T_MM01_003_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 003 R", "0:100 1:100", "A:849037687;C:754289116;G:741157518;T:854195808;N:1319871", 100, 100, null, null, 849037687, 754289116, 741157518, 854195808, 1319871, "ERX552371", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93418, 0.93244, 0.09187, 0.09177, 0.67919, 0.68278, 0.49475, 0.4843, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15056, "ERR594442", "ERX552370", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 013", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_013_R1.fastq.gz McGrail_PT_MM02_013_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 013 R", "0:100 1:100", "A:871688870;C:733183478;G:727799783;T:867055926;N:271943", 100, 100, null, null, 871688870, 733183478, 727799783, 867055926, 271943, "ERX552370", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92516, 0.92506, 0.12387, 0.12596, 0.69601, 0.69852, 0.49866, 0.50071, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15057, "ERR594438", "ERX552369", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 005", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_005_R1.fastq.gz McGrail_T_MM01_005_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 005 R", "0:100 1:100", "A:849484270;C:753864282;G:741293874;T:854126120;N:1231454", 100, 100, null, null, 849484270, 753864282, 741293874, 854126120, 1231454, "ERX552369", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93385, 0.93181, 0.09285, 0.0935, 0.67882, 0.68209, 0.48445, 0.49581, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15058, "ERR594452", "ERX552408", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 001", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_001_R1.fastq.gz McGrail_PT_MM02_001_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 001 R", "0:100 1:100", "A:869685021;C:734763957;G:726895796;T:867397539;N:1257687", 100, 100, null, null, 869685021, 734763957, 726895796, 867397539, 1257687, "ERX552408", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92687, 0.92533, 0.12345, 0.12461, 0.69749, 0.70055, 0.49809, 0.49848, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15059, "ERR594446", "ERX552407", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 006", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_006_R1.fastq.gz McGrail_T_MM01_006_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 006 R", "0:100 1:100", "A:850456499;C:753116092;G:742193025;T:853616872;N:617512", 100, 100, null, null, 850456499, 753116092, 742193025, 853616872, 617512, "ERX552407", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.9331, 0.93179, 0.09172, 0.09219, 0.67917, 0.68158, 0.48168, 0.48339, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15060, "ERR594428", "ERX552406", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 008", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_008_R1.fastq.gz McGrail_PT_MM02_008_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 008 R", "0:100 1:100", "A:871557679;C:733260378;G:727404860;T:867366205;N:410878", 100, 100, null, null, 871557679, 733260378, 727404860, 867366205, 410878, "ERX552406", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92806, 0.92602, 0.12481, 0.12546, 0.69771, 0.70086, 0.50152, 0.50006, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15061, "ERR594423", "ERX552405", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 008", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_008_R1.fastq.gz MM03_WT_L003_008_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 008 R", "0:100 1:100", "A:894053419;C:711591129;G:702881160;T:891029747;N:444545", 100, 100, null, null, 894053419, 711591129, 702881160, 891029747, 444545, "ERX552405", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91542, 0.91567, 0.14469, 0.14612, 0.71289, 0.7161, 0.49104, 0.48972, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15062, "ERR594424", "ERX552404", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 005", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_005_R1.fastq.gz MM03_WT_L003_005_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 005 R", "0:100 1:100", "A:892331319;C:712533931;G:701570336;T:891914366;N:1650048", 100, 100, null, null, 892331319, 712533931, 701570336, 891914366, 1650048, "ERX552404", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91746, 0.91624, 0.14471, 0.14581, 0.71498, 0.71985, 0.48939, 0.49411, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15063, "ERR594416", "ERX552403", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 005", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_005_R1.fastq.gz McGrail_PT_MM02_005_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 005 R", "0:100 1:100", "A:870557258;C:733600250;G:726156781;T:868210376;N:1475335", 100, 100, null, null, 870557258, 733600250, 726156781, 868210376, 1475335, "ERX552403", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92621, 0.92323, 0.12426, 0.1247, 0.69836, 0.70418, 0.50259, 0.49996, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15064, "ERR594427", "ERX552384", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 009", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_009_R1.fastq.gz McGrail_PT_MM02_009_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 009 R", "0:100 1:100", "A:872849771;C:731277001;G:727186355;T:868245858;N:441015", 100, 100, null, null, 872849771, 731277001, 727186355, 868245858, 441015, "ERX552384", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92396, 0.92581, 0.12417, 0.12625, 0.69879, 0.70189, 0.50046, 0.50188, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15065, "ERR594432", "ERX552383", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 010", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_010_R1.fastq.gz McGrail_T_MM01_010_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 010 R", "0:100 1:100", "A:850551531;C:753023540;G:742554950;T:852763762;N:1106217", 100, 100, null, null, 850551531, 753023540, 742554950, 852763762, 1106217, "ERX552383", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93373, 0.93132, 0.09087, 0.09072, 0.67898, 0.68083, 0.49414, 0.48713, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15066, "ERR594435", "ERX552382", "ERS539974", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM01 T", "SAMEA2747166", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail T MM01 009", "MM01 T", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_T_MM01_009_R1.fastq.gz McGrail_T_MM01_009_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail T MM01 009 R", "0:100 1:100", "A:852308329;C:751198229;G:741341036;T:854788512;N:363894", 100, 100, null, null, 852308329, 751198229, 741341036, 854788512, 363894, "ERX552382", "ERS539974", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.93348, 0.93139, 0.09329, 0.09409, 0.68071, 0.68359, 0.48469, 0.49176, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15067, "ERR594421", "ERX552381", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 012", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_012_R1.fastq.gz MM03_WT_L003_012_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 012 R", "0:100 1:100", "A:894330816;C:710946707;G:702107786;T:892049601;N:565090", 100, 100, null, null, 894330816, 710946707, 702107786, 892049601, 565090, "ERX552381", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91723, 0.91629, 0.14541, 0.14611, 0.71427, 0.71719, 0.49682, 0.49865, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15068, "ERR594451", "ERX552380", "ERS539976", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM03 WT", "SAMEA2747168", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:MM03 WT L003 001", "MM03 WT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "MM03_WT_L003_001_R1.fastq.gz MM03_WT_L003_001_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:MM03 WT L003 001 R", "0:100 1:100", "A:892492791;C:713070365;G:702444959;T:891434993;N:556892", 100, 100, null, null, 892492791, 713070365, 702444959, 891434993, 556892, "ERX552380", "ERS539976", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.91795, 0.91727, 0.14627, 0.14672, 0.71382, 0.71636, 0.48819, 0.49971, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15069, "ERR594448", "ERX552379", "ERS539975", "ERP006866", "PRJEB7172", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E-MTAB-2886", "Transcriptome Analysis", "Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina  optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.", null, null, "Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "MM02 PT", "SAMEA2747167", "Iowa State University", "ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "E MTAB 2886:McGrail PT MM02 003", "MM02 PT", "Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample  \u201cWild Type\u201d  contained three pooled retinas from 6 mpf wild type adults. The second sample  \u201cPretumor\u201d  consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample  \u201cTumor\u201d  consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced  large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource  Duke Institute for Genome Sciences and Policy  Duke University.", "Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><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_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "ERP006866", "Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line", "ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16", "McGrail_PT_MM02_003_R1.fastq.gz McGrail_PT_MM02_003_R2.fastq.gz", "fastq fastq", 3200000000.0, 16000000.0, "E MTAB 2886:McGrail PT MM02 003 R", "0:100 1:100", "A:870188856;C:734020429;G:726554216;T:867996712;N:1239787", 100, 100, null, null, 870188856, 734020429, 726554216, 867996712, 1239787, "ERX552379", "ERS539975", "ERA356220", "Iowa State University", "Iowa State University", 2, 0.92516, 0.92471, 0.12313, 0.12411, 0.69686, 0.69982, 0.49257, 0.49644, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2014-12-11", "Adult", "Adult", "Multi-tissue", "Multi-system"], [15394, "ERR12724517", "ERX12099016", "ERS18400121", "ERP158370", "PRJEB73599", "RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings", "E-MTAB-13886", "Transcriptome Analysis", "Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants.   The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted.", "ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29", null, "Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen  74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. 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Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen  74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. 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Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen  74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. 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