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56 rows where experiment.library_selection = "PolyA" and technology = "bulk"

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tissue_curation 6

devstage_curation_coarse 3

devstage_curation 3

technology 1

  • bulk · 56 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 56 ✖

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
6 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.       wildtype sibling sample4 SAMD00400823   sample name:rw147 2.5dpf wildtype rep 4|biological replicate:4                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400823 DRX305194 1 1 1   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       10262353995.0 34151547.0 DRR315802 0:150.27 1:150.22 A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
7 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.       wildtype sibling sample3 SAMD00400822   sample name:rw147 2.5dpf wildtype rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400822 DRX305193 1 1 1   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       11516368634.0 38355888.0 DRR315801 0:150.15 1:150.10 A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
8 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.       wildtype sibling sample2 SAMD00400821   sample name:rw147 2.5dpf wildtype rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400821 DRX305192 1 1 1   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       8814057148.0 29367513.0 DRR315800 0:150.09 1:150.04 A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
9 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.       wildtype sibling sample1 SAMD00400820   sample name:rw147 2.5dpf wildtype rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400820 DRX305191 1 1 1   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       10491955578.0 34900682.0 DRR315799 0:150.34 1:150.28 A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
10 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.       strip1 mutant sample4 SAMD00400819   sample name:rw147 2.5dpf Mutant rep 4|biological replicate:4                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400819 DRX305190 1 1 1   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       9197802250.0 30604326.0 DRR315798 0:150.30 1:150.24 A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
11 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.       strip1 mutant sample3 SAMD00400818   sample name:rw147 2.5dpf Mutant rep 3|biological replicate:3                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400818 DRX305189 1 1 1   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       10498982078.0 34931731.0 DRR315797 0:150.31 1:150.25 A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
12 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.       strip1 mutant sample2 SAMD00400817   sample name:rw147 2.5dpf Mutant rep 2|biological replicate:2                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400817 DRX305188 1 1 1   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       9850145990.0 32782079.0 DRR315796 0:150.26 1:150.21 A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
13 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.       strip1 mutant sample1 SAMD00400816   sample name:rw147 2.5dpf Mutant rep 1|biological replicate:1                 Illumina NovaSeq 6000 paired end sequencing of SAMD00400816 DRX305187 1 1 1   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       9542039835.0 31780260.0 DRR315795 0:150.15 1:150.10 A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225 150 150     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   Unknown 2022-03-16 Hatching Embryo Undetermined Embryo Imprecise
9699 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9700 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9701 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9702 9702 ERR3301003 ERX3327070 ERS3389658 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… WT heart rep 3 SAMEA5585434 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585434|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:6|organism part:heart|sample name:E MTAB 7920:WT heart rep 3|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT heart rep 3 p WT heart rep 3 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz fastq fastq 7339830080.0 45873938.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3 0:80 1:80 A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141 80 80     1985328994 1673818891 1695753386 1984031668 897141 ERX3327070 ERS3389658 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.9311 0.94858 0.07774 0.07789 0.76378 0.76394 0.52815 0.52065 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
9703 9703 ERR3301002 ERX3327069 ERS3389657 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… WT heart rep 2 SAMEA5585433 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585433|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:5|organism part:heart|sample name:E MTAB 7920:WT heart rep 2|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT heart rep 2 p WT heart rep 2 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz fastq fastq 7486415840.0 46790099.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2 0:80 1:80 A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493 80 80     2020798219 1702752807 1731176796 2030756525 931493 ERX3327069 ERS3389657 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93397 0.9509 0.07752 0.07859 0.76019 0.76002 0.54034 0.54728 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
9704 9704 ERR3301001 ERX3327068 ERS3389656 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… WT heart rep 1 SAMEA5585432 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585432|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:4|organism part:heart|sample name:E MTAB 7920:WT heart rep 1|scientific name:Danio rerio|sex:female|strain:AB                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:WT heart rep 1 p WT heart rep 1 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz fastq fastq 6814600800.0 42591255.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1 0:80 1:80 A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985 80 80     1823108307 1567497576 1587567005 1835589927 837985 ERX3327068 ERS3389656 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93109 0.94806 0.07581 0.07635 0.75907 0.75988 0.54746 0.54753 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
9705 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9706 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9707 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   Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. T… 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                 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®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA 2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples … 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   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     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   Ireland 2019-04-30 Larval Larval Whole Organism All anatomical structures
9708 9708 ERR3300997 ERX3327064 ERS3389652 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… Mutant heart rep 3 SAMEA5585428 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585428|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:3|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 3|scientific name:Danio rerio|sex:female|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant heart rep 3 p Mutant heart rep 3 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz fastq fastq 7240447520.0 45252797.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3 0:80 1:80 A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957 80 80     1968283412 1645458614 1652590010 1973242527 872957 ERX3327064 ERS3389652 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.92784 0.94597 0.08601 0.08686 0.76702 0.76449 0.50929 0.52685 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
9709 9709 ERR3300996 ERX3327063 ERS3389651 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… Mutant heart rep 2 SAMEA5585427 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585427|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:2|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 2|scientific name:Danio rerio|sex:female|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant heart rep 2 p Mutant heart rep 2 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz fastq fastq 7347029600.0 45918935.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2 0:80 1:80 A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229 80 80     1967915665 1690507331 1712776156 1974918219 912229 ERX3327063 ERS3389651 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93337 0.94978 0.07673 0.07724 0.76755 0.76798 0.53415 0.51157 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
9710 9710 ERR3300995 ERX3327062 ERS3389650 ERP115040 PRJEB32363 RNA seq of zebrafish sa12692 mutants against WT controls E-MTAB-7920 Transcriptome Analysis Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence the molecular effect of the mutation could be profiled at two life stages. ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30   Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend th… Mutant heart rep 1 SAMEA5585426 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway ENA FIRST PUBLIC:2021 04 30T00:25:02Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585426|INSDC center name:Dept. of Pharmacology and Therapeutics College of Medicine Nursing and Heath Sciences National University of Ireland Galway|INSDC first public:2021 04 30T00:25:02Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:1|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 1|scientific name:Danio rerio|sex:female|strain:sa12692 mutant                 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls E MTAB 7920:Mutant heart rep 1 p Mutant heart rep 1 p RNA seq of zebrafish sa12692 mutants against WT controls Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. T… Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 500   ERP115040 NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30 HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz fastq fastq 6296502880.0 39353143.0 E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1 0:80 1:80 A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941 80 80     1677737687 1460767489 1468915029 1688319734 762941 ERX3327062 ERS3389650 ERA1880314 Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive 2 0.93775 0.9516 0.07994 0.08077 0.75844 0.75759 0.51937 0.52207 80 80 B B biological fallback assumption illumina nextseq 3prime poly_a trueseq bulk bulk bulk   Ireland 2019-04-30 Adult Adult Multi-tissue Multi-system
10216 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10217 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10218 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10219 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10220 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
10221 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   Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C 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 μg/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°C 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°C 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 μg/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                 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°C 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 μg/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°C 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°C 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 μg/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   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     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   United Kingdom 2021-10-01 Larval Larval Heart Cardiovascular System
34192 34192 SRR31443228 SRX26812023 SRS23296672 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 3 srrm4[y712] mutant replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut3.pass2Aligned.sortedByCoord.out.bam bam 23466336192.0 117587529.0 25938 mut3.pass2Aligned.sortedByCoord.out.bam 0:100.13 1:100.08 A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927 100 100     6298034402 5433884683 5344985734 6388443446 987927 SRX26812023 SRS23296672 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95864 0.95894 0.10681 0.1052 0.65385 0.65403 0.46511 0.46252 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34193 34193 SRR31443229 SRX26812022 SRS23296671 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 3   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 3 srrm4[y712] wild type replicate 3 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt3.pass2Aligned.sortedByCoord.out.bam bam 23979171134.0 120156039.0 25938 wt3.pass2Aligned.sortedByCoord.out.bam 0:100.12 1:100.07 A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857 100 100     6398807397 5589997524 5503127729 6486232627 1005857 SRX26812022 SRS23296671 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.95941 0.96004 0.10323 0.10191 0.65451 0.6532 0.46396 0.46398 101 100 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34194 34194 SRR31443230 SRX26812021 SRS23296670 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 2 srrm4[y712] mutant replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut2.pass2Aligned.sortedByCoord.out.bam bam 20256127500.0 101792067.0 25938 mut2.pass2Aligned.sortedByCoord.out.bam 0:100.05 1:100.00 A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366 100 100     5435798119 4683997479 4650293108 5485187428 851366 SRX26812021 SRS23296670 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96008 0.96049 0.10232 0.10156 0.66072 0.65932 0.4668 0.46817 95 95 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34195 34195 SRR31443231 SRX26812020 SRS23296669 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 2   strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 2 srrm4[y712] wild type replicate 2 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt2.pass2Aligned.sortedByCoord.out.bam bam 22698373371.0 113599687.0 25938 wt2.pass2Aligned.sortedByCoord.out.bam 0:100.18 1:100.12 A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128 100 100     6063922145 5275724786 5212055837 6145709475 961128 SRX26812020 SRS23296669 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.96129 0.96063 0.1003 0.09861 0.65744 0.65748 0.46167 0.46817 98 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34196 34196 SRR31443232 SRX26812019 SRS23296667 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] mutant replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] mutant replicate 1 srrm4[y712] mutant replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_mut.pass2Aligned.sortedByCoord.out.bam bam 11282501509.0 56702666.0 25938 mut.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.55 A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849 99 99     2764745971 2868447715 2856237429 2792914545 155849 SRX26812019 SRS23296667 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development                       B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
34197 34197 SRR31443233 SRX26812018 SRS23296668 SRP546978 PRJNA1189474 Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf PRJNA1189474 Other The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses Total RNA was isolated for sequencing at 3 dpf         srrm4[y712] wild type replicate 1   strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae srrm4[y712] wild type replicate 1 srrm4[y712] wild type replicate 1 TruSeq library     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP546978   assembly:GRCz11 25938_wt.pass2Aligned.sortedByCoord.out.bam bam 16346812838.0 82104499.0 25938 wt.pass2Aligned.sortedByCoord.out.bam 0:99.65 1:99.56 A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992 99 99     3996717287 4167381503 4130586142 4051899914 227992 SRX26812018 SRS23296668 SRA2019780 Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology Eunice Kennedy Shriver National Institute of Child Health and Human Development 2 0.97776 0.97907 0.04095 0.04006 0.6702 0.67034 0.46611 0.46144 99 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk bulk bulk   United States 2024-11-22 Larval Larval Head Nervous System
35941 35941 SRR33299145 SRX28544240 SRS24843420 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT4 ppat liver   strain:ppat|isolate:RNA wt4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt4 RNA wt4 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT4_ppat-liver_S28_R1_001.fastq.gz WT4_ppat-liver_S28_R2_001.fastq.gz fastq fastq 12054556418.0 60504917.0 WT4 ppat liver S28 R1 001.fastq.gz 0:99.62 1:99.61 A:3156096964;C:2870076825;G:2908548000;T:3118003046;N:1831583 99 99     3156096964 2870076825 2908548000 3118003046 1831583 SRX28544240 SRS24843420 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35942 35942 SRR33299146 SRX28544239 SRS24843419 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT3 ppat liver   strain:ppat|isolate:RNA wt3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt3 RNA wt3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT3_ppat-liver_S27_R1_001.fastq.gz WT3_ppat-liver_S27_R2_001.fastq.gz fastq fastq 13917840876.0 69735355.0 WT3 ppat liver S27 R1 001.fastq.gz 0:99.76 1:99.82 A:3668835621;C:3297107084;G:3353446119;T:3593656283;N:4795769 99 99     3668835621 3297107084 3353446119 3593656283 4795769 SRX28544239 SRS24843419 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35943 35943 SRR33299147 SRX28544238 SRS24843418 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT2 ppat liver   strain:ppat|isolate:RNA wt2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt2 RNA wt2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT2_ppat-liver_S26_R1_001.fastq.gz WT2_ppat-liver_S26_R2_001.fastq.gz fastq fastq 13414385259.0 67138074.0 WT2 ppat liver S26 R1 001.fastq.gz 0:99.79 1:100.01 A:3544883230;C:3160905311;G:3259087045;T:3439671703;N:9837970 99 100     3544883230 3160905311 3259087045 3439671703 9837970 SRX28544238 SRS24843418 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35944 35944 SRR33299148 SRX28544237 SRS24843417 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT1 ppat liver   strain:ppat|isolate:RNA wt1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt1 RNA wt1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT1_ppat-liver_S25_R1_001.fastq.gz WT1_ppat-liver_S25_R2_001.fastq.gz fastq fastq 10922184332.0 54765335.0 WT1 ppat liver S25 R1 001.fastq.gz 0:99.61 1:99.82 A:2868583271;C:2597837660;G:2681619273;T:2767298124;N:6846004 99 99     2868583271 2597837660 2681619273 2767298124 6846004 SRX28544237 SRS24843417 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35945 35945 SRR33299149 SRX28544236 SRS24843416 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut4 ppat liver   strain:ppat|isolate:RNA mut4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut4 RNA mut4 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mut4_ppat-liver_S36_R1_001.fastq.gz Mut4_ppat-liver_S36_R2_001.fastq.gz fastq fastq 12530931476.0 62826169.0 Mut4 ppat liver S36 R1 001.fastq.gz 0:99.67 1:99.78 A:3324393503;C:2939109258;G:3014385499;T:3247670290;N:5372926 99 99     3324393503 2939109258 3014385499 3247670290 5372926 SRX28544236 SRS24843416 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35946 35946 SRR33299150 SRX28544235 SRS24843415 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut3 ppat liver   strain:ppat|isolate:RNA mut3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut3 RNA mut3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mut3_ppat-liver_S35_R1_001.fastq.gz Mut3_ppat-liver_S35_R2_001.fastq.gz fastq fastq 10720402854.0 53894468.0 Mut3 ppat liver S35 R1 001.fastq.gz 0:99.40 1:99.52 A:2864014346;C:2503521968;G:2584948225;T:2763732849;N:4185466 99 99     2864014346 2503521968 2584948225 2763732849 4185466 SRX28544235 SRS24843415 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35947 35947 SRR33299151 SRX28544234 SRS24843414 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut2 ppat liver   strain:ppat|isolate:RNA mut2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut2 RNA mut2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mut2_ppat-liver_S34_R1_001.fastq.gz Mut2_ppat-liver_S34_R2_001.fastq.gz fastq fastq 13658984938.0 68656301.0 Mut2 ppat liver S34 R1 001.fastq.gz 0:99.35 1:99.59 A:3634178483;C:3189694846;G:3300982525;T:3525339026;N:8790058 99 99     3634178483 3189694846 3300982525 3525339026 8790058 SRX28544234 SRS24843414 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35948 35948 SRR33299152 SRX28544233 SRS24843413 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut1 ppat liver   strain:ppat|isolate:RNA mut1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut1 RNA mut1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mut1_ppat-liver_S33_R1_001.fastq.gz Mut1_ppat-liver_S33_R2_001.fastq.gz fastq fastq 10934728288.0 54995591.0 Mut1 ppat liver S33 R1 001.fastq.gz 0:99.36 1:99.47 A:2909267644;C:2564520996;G:2638675283;T:2818803981;N:3460384 99 99     2909267644 2564520996 2638675283 2818803981 3460384 SRX28544233 SRS24843413 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35949 35949 SRR33299154 SRX28544231 SRS24843411 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Het4 ppat liver   strain:ppat|isolate:RNA het4|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA het4 RNA het4 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Het4_ppat-liver_S32_R1_001.fastq.gz Het4_ppat-liver_S32_R2_001.fastq.gz fastq fastq 11933665535.0 59956025.0 Het4 ppat liver S32 R1 001.fastq.gz 0:99.47 1:99.57 A:3167338389;C:2796677179;G:2888967002;T:3076290728;N:4392237 99 99     3167338389 2796677179 2888967002 3076290728 4392237 SRX28544231 SRS24843411 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35950 35950 SRR33299155 SRX28544230 SRS24843410 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Het3 ppat liver   strain:ppat|isolate:RNA het3|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA het3 RNA het3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Het3_ppat-liver_S31_R1_001.fastq.gz Het3_ppat-liver_S31_R2_001.fastq.gz fastq fastq 8736836848.0 43909775.0 Het3 ppat liver S31 R1 001.fastq.gz 0:99.49 1:99.48 A:2316148154;C:2054859781;G:2098968973;T:2265744694;N:1115246 99 99     2316148154 2054859781 2098968973 2265744694 1115246 SRX28544230 SRS24843410 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35951 35951 SRR33299156 SRX28544229 SRS24843409 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Het2 ppat liver   strain:ppat|isolate:RNA het2|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA het2 RNA het2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Het2_ppat-liver_S30_R1_001.fastq.gz Het2_ppat-liver_S30_R2_001.fastq.gz fastq fastq 7931230506.0 39763891.0 Het2 ppat liver S30 R1 001.fastq.gz 0:99.72 1:99.74 A:2118901869;C:1861115765;G:1903240420;T:2046832152;N:1140300 99 99     2118901869 1861115765 1903240420 2046832152 1140300 SRX28544229 SRS24843409 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35952 35952 SRR33299157 SRX28544228 SRS24843408 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Het1 ppat liver   strain:ppat|isolate:RNA het1|age:adult|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA het1 RNA het1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Het1_ppat-liver_S29_R1_001.fastq.gz Het1_ppat-liver_S29_R2_001.fastq.gz fastq fastq 8695997521.0 43696765.0 Het1 ppat liver S29 R1 001.fastq.gz 0:99.39 1:99.62 A:2300583830;C:2047586482;G:2114382364;T:2227671389;N:5773456 99 99     2300583830 2047586482 2114382364 2227671389 5773456 SRX28544228 SRS24843408 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Adult Adult Liver Liver and Biliary System
35953 35953 SRR33299171 SRX28544214 SRS24843394 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT pos 3   strain:ppat|isolate:RNA wt pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt pos 3 RNA wt pos 3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-pos-3_S10_R1_001.fastq.gz WT-pos-3_S10_R2_001.fastq.gz fastq fastq 15038194818.0 74446509.0 WT pos 3 S10 R1 001.fastq.gz 0:101 1:101 A:4616878123;C:2865206674;G:2927449871;T:4628427327;N:232823 101 101     4616878123 2865206674 2927449871 4628427327 232823 SRX28544214 SRS24843394 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35954 35954 SRR33299172 SRX28544213 SRS24843393 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT pos 2   strain:ppat|isolate:RNA wt pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt pos 2 RNA wt pos 2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-pos-2_S6_R1_001.fastq.gz WT-pos-2_S6_R2_001.fastq.gz fastq fastq 12522438742.0 61992271.0 WT pos 2 S6 R1 001.fastq.gz 0:101 1:101 A:3774656054;C:2451528285;G:2501043573;T:3795016419;N:194411 101 101     3774656054 2451528285 2501043573 3795016419 194411 SRX28544213 SRS24843393 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35955 35955 SRR33299173 SRX28544212 SRS24843392 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT pos 1   strain:ppat|isolate:RNA wt pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt pos 1 RNA wt pos 1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-pos-1_S2_R1_001.fastq.gz WT-pos-1_S2_R2_001.fastq.gz fastq fastq 13192760794.0 65310697.0 WT pos 1 S2 R1 001.fastq.gz 0:101 1:101 A:4175600031;C:2392141464;G:2448567492;T:4176248719;N:203088 101 101     4175600031 2392141464 2448567492 4176248719 203088 SRX28544212 SRS24843392 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35956 35956 SRR33299174 SRX28544211 SRS24843391 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT neg 3   strain:ppat|isolate:RNA wt neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt neg 3 RNA wt neg 3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-neg-3_S9_R1_001.fastq.gz WT-neg-3_S9_R2_001.fastq.gz fastq fastq 14228466708.0 70437954.0 WT neg 3 S9 R1 001.fastq.gz 0:101 1:101 A:4251988096;C:2825656049;G:2882063617;T:4268538044;N:220902 101 101     4251988096 2825656049 2882063617 4268538044 220902 SRX28544211 SRS24843391 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35957 35957 SRR33299176 SRX28544209 SRS24843389 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT neg 2   strain:ppat|isolate:RNA wt neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt neg 2 RNA wt neg 2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-neg-2_S5_R1_001.fastq.gz WT-neg-2_S5_R2_001.fastq.gz fastq fastq 29197644388.0 144542794.0 WT neg 2 S5 R1 001.fastq.gz 0:101 1:101 A:8825536643;C:5697075068;G:5851684325;T:8822896313;N:452039 101 101     8825536643 5697075068 5851684325 8822896313 452039 SRX28544209 SRS24843389 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35958 35958 SRR33299177 SRX28544208 SRS24843388 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         WT neg 1   strain:ppat|isolate:RNA wt neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA wt neg 1 RNA wt neg 1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     WT-neg-1_S1_R1_001.fastq.gz WT-neg-1_S1_R2_001.fastq.gz fastq fastq 24310317816.0 120348108.0 WT neg 1 S1 R1 001.fastq.gz 0:101 1:101 A:7529245228;C:4579294064;G:4681930604;T:7519470895;N:377025 101 101     7529245228 4579294064 4681930604 7519470895 377025 SRX28544208 SRS24843388 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35959 35959 SRR33299178 SRX28544207 SRS24843387 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut pos 3   strain:ppat|isolate:RNA mut pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut pos 3 RNA mut pos 3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-pos-3_S12_R1_001.fastq.gz Mutant-pos-3_S12_R2_001.fastq.gz fastq fastq 12331802050.0 61048525.0 Mutant pos 3 S12 R1 001.fastq.gz 0:101 1:101 A:3738975619;C:2387112788;G:2450941491;T:3754579907;N:192245 101 101     3738975619 2387112788 2450941491 3754579907 192245 SRX28544207 SRS24843387 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35960 35960 SRR33299179 SRX28544206 SRS24843386 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut pos 2   strain:ppat|isolate:RNA mut pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut pos 2 RNA mut pos 2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-pos-2_S8_R1_001.fastq.gz Mutant-pos-2_S8_R2_001.fastq.gz fastq fastq 14310451034.0 70843817.0 Mutant pos 2 S8 R1 001.fastq.gz 0:101 1:101 A:4323214668;C:2795555578;G:2854780783;T:4336680703;N:219302 101 101     4323214668 2795555578 2854780783 4336680703 219302 SRX28544206 SRS24843386 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35961 35961 SRR33299180 SRX28544205 SRS24843385 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut pos 1   strain:ppat|isolate:RNA mut pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut pos 1 RNA mut pos 1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-pos-1_S4_R1_001.fastq.gz Mutant-pos-1_S4_R2_001.fastq.gz fastq fastq 11742623802.0 58131801.0 Mutant pos 1 S4 R1 001.fastq.gz 0:101 1:101 A:3631609351;C:2213363935;G:2258388450;T:3639080712;N:181354 101 101     3631609351 2213363935 2258388450 3639080712 181354 SRX28544205 SRS24843385 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35962 35962 SRR33299181 SRX28544204 SRS24843384 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut neg 3   strain:ppat|isolate:RNA mut neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut neg 3 RNA mut neg 3 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-neg-3_S11_R1_001.fastq.gz Mutant-neg-3_S11_R2_001.fastq.gz fastq fastq 24089537270.0 119255135.0 Mutant neg 3 S11 R1 001.fastq.gz 0:101 1:101 A:7187277815;C:4790199860;G:4897671441;T:7214028116;N:360038 101 101     7187277815 4790199860 4897671441 7214028116 360038 SRX28544204 SRS24843384 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35963 35963 SRR33299182 SRX28544203 SRS24843383 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut neg 2   strain:ppat|isolate:RNA mut neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut neg 2 RNA mut neg 2 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-neg-2_S7_R1_001.fastq.gz Mutant-neg-2_S7_R2_001.fastq.gz fastq fastq 27776865470.0 137509235.0 Mutant neg 2 S7 R1 001.fastq.gz 0:101 1:101 A:8522694394;C:5302545250;G:5464259742;T:8486935677;N:430407 101 101     8522694394 5302545250 5464259742 8486935677 430407 SRX28544203 SRS24843383 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System
35964 35964 SRR33299183 SRX28544202 SRS24843382 SRP580984 PRJNA1255065 A Novel Transgenic Reporter to Study Vertebrate Epigenetics PRJNA1255065 Other Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.         Mut neg 1   strain:ppat|isolate:RNA mut neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal                 RNAseq of EpiTag Danio Rerio RNA mut neg 1 RNA mut neg 1 Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP580984     Mutant-neg-1_S3_R1_001.fastq.gz Mutant-neg-1_S3_R2_001.fastq.gz fastq fastq 12942402802.0 64071301.0 Mutant neg 1 S3 R1 001.fastq.gz 0:101 1:101 A:3952970077;C:2483104981;G:2560604982;T:3945521897;N:200865 101 101     3952970077 2483104981 2560604982 3945521897 200865 SRX28544202 SRS24843382 SRA2117853 NIH|NICHD NIH                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   United States 2025-04-24 Larval Larval Liver Liver and Biliary System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;