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2,510 rows where experiment.library_layout = "PAIRED" and technology = "bulk"

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tissue_curation >10

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  • bulk · 2,510 ✖

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  • PAIRED · 2,510 ✖
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
10391 10391 ERR8516975 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X4_190227_A00421_38_AH7523DRXX_S56_R1_001.fastq.gz 15812X4_190227_A00421_38_AH7523DRXX_S56_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X4 190227 A00421 38 AH7523DRXX S56 R 0:51 1:51 A:1077092958;C:949537387;G:955020348;T:1099432979;N:20556852 51 51     1077092958 949537387 955020348 1099432979 20556852 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.9053 0.9259 0.21658 0.22155 0.69369 0.69179 0.50726 0.50871 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10392 10392 ERR8516976 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X5_190227_A00421_38_AH7523DRXX_S55_R1_001.fastq.gz 15812X5_190227_A00421_38_AH7523DRXX_S55_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X5 190227 A00421 38 AH7523DRXX S55 R 0:51 1:51 A:972081222;C:890179393;G:888655698;T:998443264;N:18934747 51 51     972081222 890179393 888655698 998443264 18934747 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86107 0.87807 0.22063 0.23029 0.70859 0.70561 0.51656 0.51946 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10393 10393 ERR8516977 ERX8083451 ERS10521298 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling neurite SAMEA12922152 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922152|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Sibling neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling neurite p Sibling neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X6_190227_A00421_38_AH7523DRXX_S54_R1_001.fastq.gz 15812X6_190227_A00421_38_AH7523DRXX_S54_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X6 190227 A00421 38 AH7523DRXX S54 R 0:51 1:51 A:728798881;C:962223604;G:958876331;T:735449513;N:17094231 51 51     728798881 962223604 958876331 735449513 17094231 ERX8083451 ERS10521298 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.54616 0.55881 0.13313 0.14036 0.84295 0.84185 0.64193 0.59762 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10394 10394 ERR8516972 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X1_190227_A00421_38_AH7523DRXX_S59_R1_001.fastq.gz 15812X1_190227_A00421_38_AH7523DRXX_S59_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X1 190227 A00421 38 AH7523DRXX S59 R 0:51 1:51 A:837274632;C:1062368015;G:1049892288;T:853310517;N:19213786 51 51     837274632 1062368015 1049892288 853310517 19213786 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.5726 0.57788 0.13781 0.14082 0.80616 0.80452 0.61581 0.60389 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10395 10395 ERR8516973 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X2_190227_A00421_38_AH7523DRXX_S58_R1_001.fastq.gz 15812X2_190227_A00421_38_AH7523DRXX_S58_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X2 190227 A00421 38 AH7523DRXX S58 R 0:51 1:51 A:897813231;C:796012893;G:794839496;T:923696030;N:17221274 51 51     897813231 796012893 794839496 923696030 17221274 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.92095 0.94156 0.18892 0.20024 0.6901 0.68905 0.49377 0.50086 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10396 10396 ERR8516974 ERX8083450 ERS10521297 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Sibling cellular SAMEA12922151 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922151|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Sibling cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq sibling +/+ and +/ |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Sibling cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Sibling cellular p Sibling cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq sibling +/+ and +/ |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X3_190227_A00421_38_AH7523DRXX_S57_R1_001.fastq.gz 15812X3_190227_A00421_38_AH7523DRXX_S57_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X3 190227 A00421 38 AH7523DRXX S57 R 0:51 1:51 A:951912827;C:1107150666;G:1086060798;T:973791571;N:20785248 51 51     951912827 1107150666 1086060798 973791571 20785248 ERX8083450 ERS10521297 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.63792 0.62667 0.18547 0.18671 0.78756 0.78549 0.59274 0.55478 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10397 10397 ERR8516969 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X10_190227_A00421_38_AH7523DRXX_S48_R1_001.fastq.gz 15812X10_190227_A00421_38_AH7523DRXX_S48_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X10 190227 A00421 38 AH7523DRXX S48 R 0:51 1:51 A:925784769;C:934445856;G:959155668;T:924080408;N:18878983 51 51     925784769 934445856 959155668 924080408 18878983 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.59503 0.61112 0.1947 0.20225 0.76512 0.76337 0.54584 0.54345 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10398 10398 ERR8516970 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X11_190227_A00421_38_AH7523DRXX_S52_R1_001.fastq.gz 15812X11_190227_A00421_38_AH7523DRXX_S52_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X11 190227 A00421 38 AH7523DRXX S52 R 0:51 1:51 A:991755033;C:864808531;G:892202564;T:992188806;N:18881958 51 51     991755033 864808531 892202564 992188806 18881958 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.86612 0.88689 0.26181 0.2728 0.7094 0.7091 0.53639 0.53906 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10399 10399 ERR8516971 ERX8083449 ERS10521296 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null neurite SAMEA12922150 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922150|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null neurite|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neurite|sample name:E MTAB 11431:Null neurite                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null neurite p Null neurite p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neurite RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X12_190227_A00421_38_AH7523DRXX_S50_R1_001.fastq.gz 15812X12_190227_A00421_38_AH7523DRXX_S50_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X12 190227 A00421 38 AH7523DRXX S50 R 0:51 1:51 A:766707527;C:798667604;G:818782599;T:773280942;N:15938306 51 51     766707527 798667604 818782599 773280942 15938306 ERX8083449 ERS10521296 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.88811 0.92834 0.21869 0.22669 0.72878 0.72604 0.55598 0.57831 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10400 10400 ERR8516966 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X7_190227_A00421_38_AH7523DRXX_S53_R1_001.fastq.gz 15812X7_190227_A00421_38_AH7523DRXX_S53_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X7 190227 A00421 38 AH7523DRXX S53 R 0:51 1:51 A:774360373;C:720215184;G:719479745;T:796239200;N:15182374 51 51     774360373 720215184 719479745 796239200 15182374 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.79643 0.81194 0.25554 0.2603 0.72236 0.72021 0.51775 0.51678 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10401 10401 ERR8516967 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X8_190227_A00421_38_AH7523DRXX_S51_R1_001.fastq.gz 15812X8_190227_A00421_38_AH7523DRXX_S51_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X8 190227 A00421 38 AH7523DRXX S51 R 0:51 1:51 A:739921027;C:667375549;G:663864111;T:764302396;N:14288091 51 51     739921027 667375549 663864111 764302396 14288091 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.90817 0.92909 0.23387 0.24814 0.70088 0.69842 0.51238 0.51267 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
10402 10402 ERR8516968 ERX8083448 ERS10521295 ERP135383 PRJEB50776 Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E-MTAB-11431 Other Zebrafish primary neurons either sfpq sibling/control +/+ +/ or null / were cultured in transwell inserts. At DIV2 for each genotype cellular and neurite tissues were separately isolated RNA extracted and total RNAseq performed. ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19   Protocols: Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Null cellular SAMEA12922149 Centre for Developmental Neurobiology, King's College London ENA first public:2022 02 19|ENA last update:2022 02 19|External Id:SAMEA12922149|INSDC center alias:Centre for Developmental Neurobiology King's College London|INSDC center name:Centre for Developmental Neurobiology King's College London|INSDC first public:2022 02 19T00:15:43Z|INSDC last update:2022 02 19T00:15:43Z|INSDC status:public|Submitter Id:E MTAB 11431:Null cellular|broker name:ArrayExpress|common name:zebrafish|genotype:sfpq null / |growth condition:transwell culture|organism part:neuron|sample name:E MTAB 11431:Null cellular                 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue E MTAB 11431:Null cellular p Null cellular p Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue Cellular and neurite tissues cultured in transwell inserts were collected separately. Cellular tissue by swabbing and neurite tissue using a cell scraper Qiagen RNeasy Micro Kit TruSeq Stranded Total RNA Library Prep Gold kit with Ribo Zero Gold depleteion Experimental Factor: genotype:sfpq null / |Experimental Factor: organism part:neuron RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP135383 Illumina NovaSeq 6000 paired end sequencing; Total RNAseq of sfpq sibling +/+ +/ and null / primary zebrafish neuron cellular and neurite tissue ENA FIRST PUBLIC:2022 02 19|ENA LAST UPDATE:2022 02 19|loader:fastq load.py 15812X9_190227_A00421_38_AH7523DRXX_S49_R1_001.fastq.gz 15812X9_190227_A00421_38_AH7523DRXX_S49_R2_001.fastq.gz fastq fastq     E MTAB 11431:15812X9 190227 A00421 38 AH7523DRXX S49 R 0:51 1:51 A:882831441;C:935213418;G:957033335;T:879085993;N:18444957 51 51     882831441 935213418 957033335 879085993 18444957 ERX8083448 ERS10521295 ERA8932807 Centre for Developmental Neurobiology, King Centre for Developmental Neurobiology, King 2 0.76218 0.7682 0.18357 0.18521 0.74444 0.74272 0.46714 0.55518 51 51 B B biological fallback assumption illumina novaseq_era unknown random_priming ribozero bulk bulk bulk   United Kingdom 2022-02-19 Undetermined Undetermined Brain Nervous System
11226 11226 ERR10368639 ERX9900562 ERS13563108 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X9 SAMEA111469072 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469072|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X9|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X9                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X9 p 16261X9 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R1_001.fastq.gz 16261X9_190815_A00421_0101_BHFL23DRXX_S2_L001_R2_001.fastq.gz fastq fastq 2686590240.0 26339120.0 E MTAB 12301:16261X9 190815 A00421 0101 BHFL23DRXX S2 L001 R 0:51 1:51 A:694597606;C:635153638;G:628248232;T:728333026;N:257738 51 51     694597606 635153638 628248232 728333026 257738 ERX9900562 ERS13563108 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94614 0.94723 0.1538 0.15109 0.70398 0.70352 0.48123 0.48168 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11227 11227 ERR10368638 ERX9900561 ERS13563107 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X8 SAMEA111469071 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469071|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X8|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X8                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X8 p 16261X8 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R1_001.fastq.gz 16261X8_190815_A00421_0101_BHFL23DRXX_S4_L001_R2_001.fastq.gz fastq fastq 15003930006.0 147097353.0 E MTAB 12301:16261X8 190815 A00421 0101 BHFL23DRXX S4 L001 R 0:51 1:51 A:3882939949;C:3570150556;G:3520942177;T:4028462946;N:1434378 51 51     3882939949 3570150556 3520942177 4028462946 1434378 ERX9900561 ERS13563107 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94373 0.94762 0.17954 0.17832 0.70299 0.70207 0.48822 0.48842 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11228 11228 ERR10368637 ERX9900560 ERS13563106 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X7 SAMEA111469070 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469070|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X7|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:snrnp70 / |organism part:whole organism|sample name:E MTAB 12301:16261X7                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X7 p 16261X7 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:snrnp70 / RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R1_001.fastq.gz 16261X7_190815_A00421_0101_BHFL23DRXX_S6_L001_R2_001.fastq.gz fastq fastq 3806643060.0 37320030.0 E MTAB 12301:16261X7 190815 A00421 0101 BHFL23DRXX S6 L001 R 0:51 1:51 A:971582421;C:919313664;G:905728446;T:1009653865;N:364664 51 51     971582421 919313664 905728446 1009653865 364664 ERX9900560 ERS13563106 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94035 0.94356 0.1661 0.16393 0.70136 0.70082 0.48294 0.48049 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11229 11229 ERR10368636 ERX9900559 ERS13563105 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X6 SAMEA111469069 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469069|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X6|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X6                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X6 p 16261X6 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R1_001.fastq.gz 16261X6_190815_A00421_0101_BHFL23DRXX_S7_L001_R2_001.fastq.gz fastq fastq 2875874598.0 28194849.0 E MTAB 12301:16261X6 190815 A00421 0101 BHFL23DRXX S7 L001 R 0:51 1:51 A:745870043;C:683782229;G:673037324;T:772909720;N:275282 51 51     745870043 683782229 673037324 772909720 275282 ERX9900559 ERS13563105 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.9435 0.94737 0.16987 0.16888 0.6983 0.69826 0.47122 0.47409 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11230 11230 ERR10368635 ERX9900558 ERS13563104 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X5 SAMEA111469068 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469068|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X5|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X5                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X5 p 16261X5 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R1_001.fastq.gz 16261X5_190815_A00421_0101_BHFL23DRXX_S8_L001_R2_001.fastq.gz fastq fastq 2656716072.0 26046236.0 E MTAB 12301:16261X5 190815 A00421 0101 BHFL23DRXX S8 L001 R 0:51 1:51 A:693979046;C:627484571;G:617505105;T:717493108;N:254242 51 51     693979046 627484571 617505105 717493108 254242 ERX9900558 ERS13563104 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94387 0.94796 0.16299 0.16183 0.69556 0.69581 0.46842 0.47334 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11231 11231 ERR10368634 ERX9900557 ERS13563103 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X4 SAMEA111469067 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469067|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X4|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:+/cyt hSNRNP70|organism part:whole organism|sample name:E MTAB 12301:16261X4                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X4 p 16261X4 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:+/cyt hSNRNP70 RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R1_001.fastq.gz 16261X4_190815_A00421_0101_BHFL23DRXX_S9_L001_R2_001.fastq.gz fastq fastq 2693177298.0 26403699.0 E MTAB 12301:16261X4 190815 A00421 0101 BHFL23DRXX S9 L001 R 0:51 1:51 A:698547378;C:640687214;G:628869192;T:724816757;N:256757 51 51     698547378 640687214 628869192 724816757 256757 ERX9900557 ERS13563103 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94101 0.94526 0.17344 0.17201 0.68619 0.68513 0.47366 0.4702 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11232 11232 ERR10368633 ERX9900556 ERS13563102 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X3 SAMEA111469066 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469066|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X3|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X3                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X3 p 16261X3 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py|options: dnus 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R1_001.fastq.gz 16261X3_190815_A00421_0101_BHFL23DRXX_S10_L001_R2_001.fastq.gz fastq fastq 3104796462.0 60878362.0 E MTAB 12301:16261X3 190815 A00421 0101 BHFL23DRXX S10 L001 R 0:51 A:803595677;C:737898133;G:731641815;T:831364716;N:296121 51       803595677 737898133 731641815 831364716 296121 ERX9900556 ERS13563102 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 1 0.94361   0.16161   0.69822   0.4647   51   B   usable mapping rate illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11233 11233 ERR10368632 ERX9900555 ERS13563101 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X2 SAMEA111469065 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469065|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X2|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X2                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X2 p 16261X2 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R1_001.fastq.gz 16261X2_190815_A00421_0101_BHFL23DRXX_S11_L001_R2_001.fastq.gz fastq fastq 2935625892.0 28780646.0 E MTAB 12301:16261X2 190815 A00421 0101 BHFL23DRXX S11 L001 R 0:51 1:51 A:759844700;C:699591057;G:694530268;T:781380766;N:279101 51 51     759844700 699591057 694530268 781380766 279101 ERX9900555 ERS13563101 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.93297 0.93744 0.16748 0.16566 0.69929 0.6996 0.4788 0.47875 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11234 11234 ERR10368631 ERX9900554 ERS13563100 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X12 SAMEA111469064 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469064|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:52Z|INSDC last update:2022 10 31T00:16:52Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X12|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X12                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X12 p 16261X12 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R1_001.fastq.gz 16261X12_190815_A00421_0101_BHFL23DRXX_S3_L001_R2_001.fastq.gz fastq fastq 7451469240.0 73053620.0 E MTAB 12301:16261X12 190815 A00421 0101 BHFL23DRXX S3 L001 R 0:51 1:51 A:1950856364;C:1747213644;G:1718730947;T:2033957057;N:711228 51 51     1950856364 1747213644 1718730947 2033957057 711228 ERX9900554 ERS13563100 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.9372 0.94118 0.20267 0.19972 0.69794 0.69735 0.47505 0.4883 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11235 11235 ERR10368630 ERX9900553 ERS13563099 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X11 SAMEA111469063 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469063|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X11|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X11                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X11 p 16261X11 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R1_001.fastq.gz 16261X11_190815_A00421_0101_BHFL23DRXX_S5_L001_R2_001.fastq.gz fastq fastq 2754589458.0 27005779.0 E MTAB 12301:16261X11 190815 A00421 0101 BHFL23DRXX S5 L001 R 0:51 1:51 A:715675810;C:652231961;G:640938288;T:745480460;N:262939 51 51     715675810 652231961 640938288 745480460 262939 ERX9900553 ERS13563099 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.93802 0.94247 0.17937 0.17728 0.70195 0.70067 0.48458 0.48364 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11236 11236 ERR10368629 ERX9900552 ERS13563098 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X10 SAMEA111469062 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469062|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X10|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:cyt hSNRNP70/ |organism part:whole organism|sample name:E MTAB 12301:16261X10                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X10 p 16261X10 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:cyt hSNRNP70/ RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R1_001.fastq.gz 16261X10_190815_A00421_0101_BHFL23DRXX_S1_L001_R2_001.fastq.gz fastq fastq 2319764682.0 22742791.0 E MTAB 12301:16261X10 190815 A00421 0101 BHFL23DRXX S1 L001 R 0:51 1:51 A:596937200;C:555502273;G:546190804;T:620912915;N:221490 51 51     596937200 555502273 546190804 620912915 221490 ERX9900552 ERS13563098 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94034 0.94451 0.1621 0.16043 0.69406 0.6928 0.4936 0.49757 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11237 11237 ERR10368628 ERX9900551 ERS13563097 ERP141667 PRJEB56699 RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E-MTAB-12301 Other It has been recently shown that SNRNP70 a major component of the spliceosome as well as other splicing regulators are found in axons. To investigate the role of SNRNP70 in axons we generated a zebrafish null mutant and found motor connectivity defects that can be partially rescued upon transgenic overexpression of cytoplasmic only human SNRNP70 cyt hSNRNP70. To understand the molecular function of the cytoplasmic pool of this splicing protein we performed this RNA seq experiment with the aim to identify mRNA transcripts whose expression is regulated by the cytoplasmic pool of SNRNP70. To do that we crossed heterozygous mutant animals that are also positive for the cyt SNRNP70 transgene. We then split embryos into four groups: i sibling ii siblings/cyt hSNRNP70 iii null iv null/cyt hSNRNP70. Total RNA was extracted from each one of the four groups three biological replicates per sample and sequenced. ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31   Protocols: Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold 16261X1 SAMEA111469061 Department of Life Sciences University of Bath ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|External Id:SAMEA111469061|INSDC center alias:Department of Life Sciences University of Bath|INSDC center name:Department of Life Sciences University of Bath|INSDC first public:2022 10 31T00:16:51Z|INSDC last update:2022 10 31T00:16:51Z|INSDC status:public|Submitter Id:E MTAB 12301:16261X1|age:28|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|disease:normal|genotype:wild type genotype|organism part:whole organism|sample name:E MTAB 12301:16261X1                 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 E MTAB 12301:16261X1 p 16261X1 p RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 Embryos were collected and raised in Danieau's solution together with 2 μΜ 4 OHΤ. Treated embryos were screened for GFP fluorescence at 24hpf and sorted into the four genotypes. Total RNA from whole embryos was isolated from each genotype group at 28hpf using a RNeasy Mini kit and eluted in nuclease free water. Total RNA was purified using Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP141667 Illumina NovaSeq 6000 paired end sequencing; RNA seq of snrnp70 mutant zebrafish and its rescue by overexpression of cytoplasmic SNRNP70 ENA FIRST PUBLIC:2022 10 31|ENA LAST UPDATE:2022 10 31|loader:fastq load.py 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R1_001.fastq.gz 16261X1_190815_A00421_0101_BHFL23DRXX_S12_L001_R2_001.fastq.gz fastq fastq 2992675512.0 29339956.0 E MTAB 12301:16261X1 190815 A00421 0101 BHFL23DRXX S12 L001 R 0:51 1:51 A:768607745;C:718646844;G:713246748;T:791888447;N:285728 51 51     768607745 718646844 713246748 791888447 285728 ERX9900551 ERS13563097 ERA18523376 Department of Life Sciences University of Bath|European Nucleotide Archive Department of Life Sciences University of Bath|European Nucleotide Archive 2 0.94414 0.94881 0.16725 0.16648 0.68909 0.68923 0.47873 0.48244 51 51 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2022-10-31 Pharyngula Embryo Whole Organism All anatomical structures
11815 11815 ERR11799086 ERX11197445 ERS16222830 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 4 SAMEA114237385 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237385|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 4|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 4|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 4 p Sample 4 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R1.fq.gz so_zf94_VW4_MDMG7_CD45lo_mhc2dab_MGA_S58_R2.fq.gz fastq fastq 19305011730.0 95569365.0 E MTAB 13228:so zf94 VW4 MDMG7 CD45lo mhc2dab MGA S58 R 0:101 1:101 A:6768262250;C:3044091042;G:2847188942;T:6645295452;N:174044 101 101     6768262250 3044091042 2847188942 6645295452 174044 ERX11197445 ERS16222830 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.57007 0.5231 0.45597 0.40582 0.91579 0.91674 0.58257 0.5625 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11816 11816 ERR11799088 ERX11197447 ERS16222832 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 6 SAMEA114237387 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237387|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 6|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 6|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 6 p Sample 6 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R2.fq.gz so_zf94_VW6_MDMF8_CD45hi_mhc2dab_MACA_S60_R1.fq.gz fastq fastq 21028230098.0 104100149.0 E MTAB 13228:so zf94 VW6 MDMF8 CD45hi mhc2dab MACA S60 R 0:101 1:101 A:6738894716;C:4007335499;G:3664578692;T:6617229148;N:192043 101 101     6738894716 4007335499 3664578692 6617229148 192043 ERX11197447 ERS16222832 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.69217 0.69414 0.45934 0.4539 0.86423 0.86344 0.64485 0.62976 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11817 11817 ERR11799085 ERX11197444 ERS16222829 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 3 SAMEA114237384 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237384|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 3|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 3|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 3 p Sample 3 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R1.fq.gz so_zf94_VW3_MDMG1_CD45lo_mhc2dab_MGA_S57_R2.fq.gz fastq fastq 20720724286.0 102577843.0 E MTAB 13228:so zf94 VW3 MDMG1 CD45lo mhc2dab MGA S57 R 0:101 1:101 A:7221245295;C:3305546836;G:3154595537;T:7039147315;N:189303 101 101     7221245295 3305546836 3154595537 7039147315 189303 ERX11197444 ERS16222829 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.6027 0.56103 0.46397 0.41738 0.90536 0.90473 0.59858 0.59246 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11818 11818 ERR11799087 ERX11197446 ERS16222831 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 5 SAMEA114237386 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237386|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 5|age:6|broker name:ArrayExpress|cell type:myeloid leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 5|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 5 p Sample 5 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R2.fq.gz so_zf94_VW5_MDMF2_CD45hi_mhc2dab_MACA_S59_R1.fq.gz fastq fastq 20557799368.0 101771284.0 E MTAB 13228:so zf94 VW5 MDMF2 CD45hi mhc2dab MACA S59 R 0:101 1:101 A:5872430236;C:4635392917;G:4244261404;T:5805533335;N:181476 101 101     5872430236 4635392917 4244261404 5805533335 181476 ERX11197446 ERS16222831 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.48524 0.49426 0.30765 0.31318 0.87008 0.86918 0.60597 0.58678 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11819 11819 ERR11799083 ERX11197442 ERS16222827 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 1 SAMEA114237382 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237382|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 1|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 1 p Sample 1 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R2.fq.gz so_zf94_VW1_P2Y12_CD45lo_MGA_S55_R1.fq.gz fastq fastq 24592452226.0 121744813.0 E MTAB 13228:so zf94 VW1 P2Y12 CD45lo MGA S55 R 0:101 1:101 A:6964719283;C:5587681189;G:5075783189;T:6964040906;N:227659 101 101     6964719283 5587681189 5075783189 6964040906 227659 ERX11197442 ERS16222827 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.82038 0.82668 0.39096 0.39605 0.82532 0.82446 0.63514 0.57014 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
11820 11820 ERR11799084 ERX11197443 ERS16222828 ERP149963 PRJEB64798 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E-MTAB-13228 Transcriptome Analysis We performed bulk transcriptomic analyses to compare the expression profile of different brain myeloid leukocytes. We used both Tgp2ry12::p2ry12 GFP; cd45:DsRed and Tgmhc2dab:GFP; cd45:DsRed adult fish allowing to FACS sort microglia identified in these animals as GFP+; DsRed+ or GFP+; DsRedlow cells respectively. Brain putative DC like cells were obtained using the Tgmhc2dab:GFP; cd45:DsRed reporter and isolated as GFP+; DsRedhigh. These analyses confirm that cd45:DsRedhigh; mhc2dab:GFP+ cells share a similar transcriptome distinct from microglia and are DC like cells. ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25   Protocols: FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set Sample 2 SAMEA114237383 Universite Libre de Bruxelles ENA FIRST PUBLIC:2023 12 25T01:15:27Z|ENA LAST UPDATE:2023 12 25T01:15:27Z|External Id:SAMEA114237383|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:27Z|INSDC last update:2023 12 25T01:15:27Z|INSDC status:public|Submitter Id:E MTAB 13228:Sample 2|age:6|broker name:ArrayExpress|cell type:microglial cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|isolate:not applicable|organism part:brain|sample name:E MTAB 13228:Sample 2|scientific name:Danio rerio|sex:male and female|strain:AB                 Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines E MTAB 13228:Sample 2 p Sample 2 p Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines FACS sorting of brain leukocytes. Approximately 8 000 microglial cells p2ry12+; cd45+ or mhc2dab+; cd45low n=2 for each Tg and 1 200 DC like cells mhc2dab+; cd45high n=2 were sorted. RNA Ovation Solo RNA Seq System NuGen TECAN with the SoLo Custom AnyDeplete Probe Mix Zebrafish probe set   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP149963 Illumina NovaSeq 6000 paired end sequencing; Transcriptomic analysis of microglia and DC like cells sorted using different reporter lines ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R2.fq.gz so_zf94_VW2_P2Y12_CD45lo_MGA_S56_R1.fq.gz fastq fastq 23692841994.0 117291297.0 E MTAB 13228:so zf94 VW2 P2Y12 CD45lo MGA S56 R 0:101 1:101 A:6997658831;C:5103576511;G:4615471075;T:6975924499;N:211078 101 101     6997658831 5103576511 4615471075 6975924499 211078 ERX11197443 ERS16222828 ERA26360556 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive 2 0.78961 0.79279 0.39456 0.39476 0.8227 0.82309 0.62072 0.61776 101 101 B B biological fallback assumption illumina novaseq_era unknown rrna_depletion unknown bulk bulk bulk   United Kingdom 2023-12-25 Adult Adult Brain Nervous System
15028 15028 ERR594449 ERX552402 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 010 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_010_R1.fastq.gz McGrail_PT_MM02_010_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 010 R 0:100 1:100 A:871527648;C:730105705;G:727172263;T:866698092;N:4496292 100 100     871527648 730105705 727172263 866698092 4496292 ERX552402 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92177 0.92501 0.1237 0.1262 0.69844 0.7009 0.49781 0.4982 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15029 15029 ERR594457 ERX552401 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 002 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_002_R1.fastq.gz McGrail_PT_MM02_002_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 002 R 0:100 1:100 A:872387737;C:732112926;G:726274702;T:868026782;N:1197853 100 100     872387737 732112926 726274702 868026782 1197853 ERX552401 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92719 0.92684 0.126 0.12696 0.69684 0.70118 0.49645 0.50037 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15030 15030 ERR594456 ERX552400 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 004 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_004_R2.fastq.gz McGrail_T_MM01_004_R1.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 004 R 0:100 1:100 A:849885320;C:752565271;G:741295555;T:853272249;N:2981605 100 100     849885320 752565271 741295555 853272249 2981605 ERX552400 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93431 0.93209 0.09121 0.09114 0.67842 0.68065 0.49543 0.48591 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15031 15031 ERR594431 ERX552399 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 014 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_014_R1.fastq.gz MM03_WT_L003_014_R2.fastq.gz fastq fastq 2051137800.0 10255689.0 E MTAB 2886:MM03 WT L003 014 R 0:100 1:100 A:574425675;C:454197762;G:448836898;T:573386204;N:291261 100 100     574425675 454197762 448836898 573386204 291261 ERX552399 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91659 0.91612 0.14679 0.14915 0.7163 0.72188 0.49275 0.49876 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15032 15032 ERR594437 ERX552398 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 006 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_006_R1.fastq.gz MM03_WT_L003_006_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 006 R 0:100 1:100 A:892528148;C:712696530;G:702466589;T:891189817;N:1118916 100 100     892528148 712696530 702466589 891189817 1118916 ERX552398 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91798 0.9161 0.14538 0.14613 0.71401 0.71656 0.48443 0.48666 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15033 15033 ERR594420 ERX552397 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 014 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_014_R1.fastq.gz McGrail_PT_MM02_014_R2.fastq.gz fastq fastq 2883852800.0 14419264.0 E MTAB 2886:McGrail PT MM02 014 R 0:100 1:100 A:787372572;C:658074713;G:654251401;T:783994205;N:159909 100 100     787372572 658074713 654251401 783994205 159909 ERX552397 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92417 0.9255 0.12479 0.12619 0.69942 0.7035 0.50149 0.49379 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15034 15034 ERR594450 ERX552396 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 014 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_014_R1.fastq.gz McGrail_T_MM01_014_R2.fastq.gz fastq fastq 632445400.0 3162227.0 E MTAB 2886:McGrail T MM01 014 R 0:100 1:100 A:168708082;C:147923885;G:146292680;T:169438791;N:81962 100 100     168708082 147923885 146292680 169438791 81962 ERX552396 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93335 0.93318 0.09287 0.09485 0.68205 0.68846 0.4841 0.49015 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15035 15035 ERR594453 ERX552395 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 011 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_011_R1.fastq.gz McGrail_T_MM01_011_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 011 R 0:100 1:100 A:852133250;C:751414688;G:741468348;T:854136333;N:847381 100 100     852133250 751414688 741468348 854136333 847381 ERX552395 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93354 0.93309 0.09259 0.09299 0.68085 0.68347 0.48686 0.48742 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15036 15036 ERR594429 ERX552394 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 002 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_002_R1.fastq.gz McGrail_T_MM01_002_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 002 R 0:100 1:100 A:851061858;C:752624348;G:741241133;T:854588994;N:483667 100 100     851061858 752624348 741241133 854588994 483667 ERX552394 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.9341 0.93285 0.09214 0.09303 0.68036 0.68465 0.4888 0.4918 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15037 15037 ERR594444 ERX552393 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 007 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_007_R1.fastq.gz McGrail_PT_MM02_007_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 007 R 0:100 1:100 A:871235248;C:733455837;G:726280934;T:868628388;N:399593 100 100     871235248 733455837 726280934 868628388 399593 ERX552393 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92587 0.9237 0.12434 0.12596 0.69729 0.70473 0.49751 0.49568 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15038 15038 ERR594436 ERX552392 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 010 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_010_R1.fastq.gz MM03_WT_L003_010_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 010 R 0:100 1:100 A:893317570;C:712391457;G:703064824;T:890653459;N:572690 100 100     893317570 712391457 703064824 890653459 572690 ERX552392 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91775 0.91713 0.14296 0.14486 0.7136 0.71638 0.50074 0.49246 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15039 15039 ERR594454 ERX552391 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 003 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_003_R1.fastq.gz MM03_WT_L003_003_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 003 R 0:100 1:100 A:891513936;C:713529681;G:702140879;T:891351829;N:1463675 100 100     891513936 713529681 702140879 891351829 1463675 ERX552391 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91714 0.91621 0.14364 0.14479 0.71384 0.71967 0.48172 0.4892 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15040 15040 ERR594422 ERX552378 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 001 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_001_R1.fastq.gz McGrail_T_MM01_001_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 001 R 0:100 1:100 A:849397709;C:754334352;G:741772141;T:853832972;N:662826 100 100     849397709 754334352 741772141 853832972 662826 ERX552378 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93478 0.93297 0.09219 0.09261 0.67949 0.68205 0.48892 0.47759 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15041 15041 ERR594433 ERX552377 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 009 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_009_R1.fastq.gz MM03_WT_L003_009_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 009 R 0:100 1:100 A:895908752;C:709459693;G:701325342;T:892915017;N:391196 100 100     895908752 709459693 701325342 892915017 391196 ERX552377 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91776 0.91744 0.14402 0.14626 0.71435 0.71794 0.48624 0.49768 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15042 15042 ERR594419 ERX552376 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 011 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_011_R1.fastq.gz MM03_WT_L003_011_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 011 R 0:100 1:100 A:894536120;C:711072714;G:702055612;T:891872676;N:462878 100 100     894536120 711072714 702055612 891872676 462878 ERX552376 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91628 0.91598 0.14427 0.14587 0.71293 0.71575 0.48688 0.49317 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15043 15043 ERR594447 ERX552375 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 004 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_004_R1.fastq.gz MM03_WT_L003_004_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 004 R 0:100 1:100 A:893087129;C:711953975;G:702111417;T:891168240;N:1679239 100 100     893087129 711953975 702111417 891168240 1679239 ERX552375 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91793 0.91708 0.14418 0.1457 0.71052 0.71405 0.50617 0.49339 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15044 15044 ERR594441 ERX552374 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 004 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_004_R1.fastq.gz McGrail_PT_MM02_004_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 004 R 0:100 1:100 A:869694755;C:734631291;G:727458512;T:866857422;N:1358020 100 100     869694755 734631291 727458512 866857422 1358020 ERX552374 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92607 0.9248 0.12414 0.12446 0.69686 0.6995 0.50202 0.50333 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15045 15045 ERR594455 ERX552373 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 002 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_002_R1.fastq.gz MM03_WT_L003_002_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 002 R 0:100 1:100 A:894222634;C:711188537;G:702167816;T:891816353;N:604660 100 100     894222634 711188537 702167816 891816353 604660 ERX552373 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.9174 0.91577 0.14516 0.14534 0.71342 0.71756 0.48084 0.50033 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15046 15046 ERR594439 ERX552410 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 007 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_007_R1.fastq.gz McGrail_T_MM01_007_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 007 R 0:100 1:100 A:850777874;C:752786693;G:741650641;T:854268527;N:516265 100 100     850777874 752786693 741650641 854268527 516265 ERX552410 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93398 0.93264 0.0917 0.09232 0.67878 0.68172 0.48311 0.48417 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15047 15047 ERR594426 ERX552409 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 012 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_012_R1.fastq.gz McGrail_T_MM01_012_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 012 R 0:100 1:100 A:851190790;C:752415289;G:742719596;T:852979263;N:695062 100 100     851190790 752415289 742719596 852979263 695062 ERX552409 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93297 0.9327 0.09093 0.09105 0.68043 0.68282 0.48563 0.48327 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15048 15048 ERR594417 ERX552390 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 007 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_007_R1.fastq.gz MM03_WT_L003_007_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 007 R 0:100 1:100 A:893566548;C:711756657;G:701577232;T:892509486;N:590077 100 100     893566548 711756657 701577232 892509486 590077 ERX552390 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.9176 0.91644 0.14542 0.14641 0.71358 0.71713 0.48742 0.50207 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15049 15049 ERR594418 ERX552389 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 008 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_008_R1.fastq.gz McGrail_T_MM01_008_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 008 R 0:100 1:100 A:851314323;C:752411525;G:742349039;T:853577153;N:347960 100 100     851314323 752411525 742349039 853577153 347960 ERX552389 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93343 0.93187 0.09175 0.09249 0.68016 0.68164 0.47952 0.48824 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15050 15050 ERR594440 ERX552388 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 013 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_013_R1.fastq.gz McGrail_T_MM01_013_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 013 R 0:100 1:100 A:852425880;C:750595968;G:742140159;T:854286637;N:551356 100 100     852425880 750595968 742140159 854286637 551356 ERX552388 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93231 0.93338 0.09134 0.09313 0.67945 0.68256 0.48693 0.48084 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15051 15051 ERR594430 ERX552387 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 006 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_006_R1.fastq.gz McGrail_PT_MM02_006_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 006 R 0:100 1:100 A:869575312;C:734964855;G:727824124;T:866586174;N:1049535 100 100     869575312 734964855 727824124 866586174 1049535 ERX552387 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.9265 0.92348 0.12368 0.12345 0.69818 0.70017 0.4966 0.50082 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15052 15052 ERR594445 ERX552386 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 012 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_012_R1.fastq.gz McGrail_PT_MM02_012_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 012 R 0:100 1:100 A:870939166;C:729921300;G:724359208;T:865762186;N:9018140 100 100     870939166 729921300 724359208 865762186 9018140 ERX552386 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92143 0.92467 0.1229 0.12533 0.69828 0.70015 0.50049 0.4981 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15053 15053 ERR594434 ERX552385 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 013 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_013_R1.fastq.gz MM03_WT_L003_013_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 013 R 0:100 1:100 A:894614606;C:711109946;G:702301073;T:891485450;N:488925 100 100     894614606 711109946 702301073 891485450 488925 ERX552385 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91697 0.91671 0.1447 0.14584 0.71327 0.7176 0.48116 0.49462 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15054 15054 ERR594443 ERX552372 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 011 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_011_R1.fastq.gz McGrail_PT_MM02_011_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 011 R 0:100 1:100 A:869080240;C:728959737;G:723451216;T:862492567;N:16016240 100 100     869080240 728959737 723451216 862492567 16016240 ERX552372 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.91732 0.92471 0.12164 0.12427 0.69739 0.69773 0.50246 0.50104 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15055 15055 ERR594425 ERX552371 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 003 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_003_R1.fastq.gz McGrail_T_MM01_003_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 003 R 0:100 1:100 A:849037687;C:754289116;G:741157518;T:854195808;N:1319871 100 100     849037687 754289116 741157518 854195808 1319871 ERX552371 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93418 0.93244 0.09187 0.09177 0.67919 0.68278 0.49475 0.4843 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15056 15056 ERR594442 ERX552370 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 013 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_013_R1.fastq.gz McGrail_PT_MM02_013_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 013 R 0:100 1:100 A:871688870;C:733183478;G:727799783;T:867055926;N:271943 100 100     871688870 733183478 727799783 867055926 271943 ERX552370 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92516 0.92506 0.12387 0.12596 0.69601 0.69852 0.49866 0.50071 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15057 15057 ERR594438 ERX552369 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 005 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_005_R1.fastq.gz McGrail_T_MM01_005_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 005 R 0:100 1:100 A:849484270;C:753864282;G:741293874;T:854126120;N:1231454 100 100     849484270 753864282 741293874 854126120 1231454 ERX552369 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93385 0.93181 0.09285 0.0935 0.67882 0.68209 0.48445 0.49581 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15058 15058 ERR594452 ERX552408 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 001 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_001_R1.fastq.gz McGrail_PT_MM02_001_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 001 R 0:100 1:100 A:869685021;C:734763957;G:726895796;T:867397539;N:1257687 100 100     869685021 734763957 726895796 867397539 1257687 ERX552408 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92687 0.92533 0.12345 0.12461 0.69749 0.70055 0.49809 0.49848 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15059 15059 ERR594446 ERX552407 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 006 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_006_R1.fastq.gz McGrail_T_MM01_006_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 006 R 0:100 1:100 A:850456499;C:753116092;G:742193025;T:853616872;N:617512 100 100     850456499 753116092 742193025 853616872 617512 ERX552407 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.9331 0.93179 0.09172 0.09219 0.67917 0.68158 0.48168 0.48339 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15060 15060 ERR594428 ERX552406 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 008 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_008_R1.fastq.gz McGrail_PT_MM02_008_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 008 R 0:100 1:100 A:871557679;C:733260378;G:727404860;T:867366205;N:410878 100 100     871557679 733260378 727404860 867366205 410878 ERX552406 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92806 0.92602 0.12481 0.12546 0.69771 0.70086 0.50152 0.50006 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15061 15061 ERR594423 ERX552405 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 008 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_008_R1.fastq.gz MM03_WT_L003_008_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 008 R 0:100 1:100 A:894053419;C:711591129;G:702881160;T:891029747;N:444545 100 100     894053419 711591129 702881160 891029747 444545 ERX552405 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91542 0.91567 0.14469 0.14612 0.71289 0.7161 0.49104 0.48972 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15062 15062 ERR594424 ERX552404 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 005 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_005_R1.fastq.gz MM03_WT_L003_005_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 005 R 0:100 1:100 A:892331319;C:712533931;G:701570336;T:891914366;N:1650048 100 100     892331319 712533931 701570336 891914366 1650048 ERX552404 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91746 0.91624 0.14471 0.14581 0.71498 0.71985 0.48939 0.49411 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15063 15063 ERR594416 ERX552403 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 005 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_005_R1.fastq.gz McGrail_PT_MM02_005_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 005 R 0:100 1:100 A:870557258;C:733600250;G:726156781;T:868210376;N:1475335 100 100     870557258 733600250 726156781 868210376 1475335 ERX552403 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92621 0.92323 0.12426 0.1247 0.69836 0.70418 0.50259 0.49996 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15064 15064 ERR594427 ERX552384 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 009 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_009_R1.fastq.gz McGrail_PT_MM02_009_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 009 R 0:100 1:100 A:872849771;C:731277001;G:727186355;T:868245858;N:441015 100 100     872849771 731277001 727186355 868245858 441015 ERX552384 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92396 0.92581 0.12417 0.12625 0.69879 0.70189 0.50046 0.50188 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15065 15065 ERR594432 ERX552383 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 010 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_010_R1.fastq.gz McGrail_T_MM01_010_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 010 R 0:100 1:100 A:850551531;C:753023540;G:742554950;T:852763762;N:1106217 100 100     850551531 753023540 742554950 852763762 1106217 ERX552383 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93373 0.93132 0.09087 0.09072 0.67898 0.68083 0.49414 0.48713 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15066 15066 ERR594435 ERX552382 ERS539974 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM01 T SAMEA2747166 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747166|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM01 T|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retinal tumor|sample name:E MTAB 2886:MM01 T|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail T MM01 009 MM01 T Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retinal tumor|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_T_MM01_009_R1.fastq.gz McGrail_T_MM01_009_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail T MM01 009 R 0:100 1:100 A:852308329;C:751198229;G:741341036;T:854788512;N:363894 100 100     852308329 751198229 741341036 854788512 363894 ERX552382 ERS539974 ERA356220 Iowa State University Iowa State University 2 0.93348 0.93139 0.09329 0.09409 0.68071 0.68359 0.48469 0.49176 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15067 15067 ERR594421 ERX552381 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 012 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_012_R1.fastq.gz MM03_WT_L003_012_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 012 R 0:100 1:100 A:894330816;C:710946707;G:702107786;T:892049601;N:565090 100 100     894330816 710946707 702107786 892049601 565090 ERX552381 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91723 0.91629 0.14541 0.14611 0.71427 0.71719 0.49682 0.49865 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15068 15068 ERR594451 ERX552380 ERS539976 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM03 WT SAMEA2747168 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747168|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM03 WT|broker name:ArrayExpress|common name:zebrafish|genotype:wild type genotype|organism part:retina|sample name:E MTAB 2886:MM03 WT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:MM03 WT L003 001 MM03 WT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 MM03_WT_L003_001_R1.fastq.gz MM03_WT_L003_001_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:MM03 WT L003 001 R 0:100 1:100 A:892492791;C:713070365;G:702444959;T:891434993;N:556892 100 100     892492791 713070365 702444959 891434993 556892 ERX552380 ERS539976 ERA356220 Iowa State University Iowa State University 2 0.91795 0.91727 0.14627 0.14672 0.71382 0.71636 0.48819 0.49971 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15069 15069 ERR594448 ERX552379 ERS539975 ERP006866 PRJEB7172 Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E-MTAB-2886 Transcriptome Analysis Heterozygous adults of the zebrafish transgenic line Tgflk1:RFPis18 develop tumors in the retina optic nerve and optic tract. Transcriptome profiling of dissected retina or retinal tumor tissue from age matched 6 mpf sibling wild type and Tgflk1:RFPis18/+ fish was generated by 100 bp paired end sequencing on an Illumina HiSeq system. 3 wild type retina were pooled to create Sample WT wild type; 3 grossly normal retina from Tgflk1:RFPis18/+ were pooled to create Sample PT pre tumor and 2 large tumors from Tgflk1:RFPis18/+ were pooled to create Sample T tumor. Each sample was run in an individual lane on the HiSeq system.     Protocols: isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. MM02 PT SAMEA2747167 Iowa State University ENA FIRST PUBLIC:2014 12 11T17:01:51Z|ENA LAST UPDATE:2018 03 08T21:23:23Z|External Id:SAMEA2747167|INSDC center name:Iowa State University|INSDC first public:2014 12 11T17:01:51Z|INSDC last update:2018 03 08T21:23:23Z|INSDC status:public|Submitter Id:E MTAB 2886:MM02 PT|broker name:ArrayExpress|common name:zebrafish|genotype:Tgflk1:RFPis18/+|organism part:retina|sample name:E MTAB 2886:MM02 PT|scientific name:Danio rerio                 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line E MTAB 2886:McGrail PT MM02 003 MM02 PT Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line isolation and care of zebrafish transgenic line Tgflk1:RFPis18 Tissues for isolation of total RNA for RNA Seq libraries were dissected from three age matched genotypes. Total RNA was isolated using Qiagen RNeasy RNA Isolation Kit Qiagen. The first sample “Wild Type” contained three pooled retinas from 6 mpf wild type adults. The second sample “Pretumor” consisted of three pooled retinas from age matched heterozygous Tgflk1:RFPis18/+ adults that did not show obvious gross ocular tumors. The third sample “Tumor” consisted of tumor tissue dissected from the eyes of two age matched heterozygous Tgflk1:RFPis18/+ adults that had advanced large tumors that filled the vitreous and distorted the ocular cavity. RNA Seq libraries were prepared from each sample and 100 bp paired end sequenced in individual lanes on an Illumina HiSeq 2000 instrument at the Genome Sequencing and Analysis Core Resource Duke Institute for Genome Sciences and Policy Duke University. Experimental Factor: organism part:retina|Experimental Factor: genotype:Tgflk1:RFPis18/+ RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> ERP006866 Illumina HiSeq 2000 paired end sequencing; Transcriptome analysis of retinal tumor onset and progression in a zebrafish optic pathway tumor line ENA FIRST PUBLIC:2014 12 11|ENA LAST UPDATE:2018 11 16 McGrail_PT_MM02_003_R1.fastq.gz McGrail_PT_MM02_003_R2.fastq.gz fastq fastq 3200000000.0 16000000.0 E MTAB 2886:McGrail PT MM02 003 R 0:100 1:100 A:870188856;C:734020429;G:726554216;T:867996712;N:1239787 100 100     870188856 734020429 726554216 867996712 1239787 ERX552379 ERS539975 ERA356220 Iowa State University Iowa State University 2 0.92516 0.92471 0.12313 0.12411 0.69686 0.69982 0.49257 0.49644 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk bulk bulk   United States 2014-12-11 Adult Adult Multi-tissue Multi-system
15394 15394 ERR12724517 ERX12099016 ERS18400121 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 WT 2 E MTAB 13886:Foxg1 WT 2   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a WT|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 WT 2 p Foxg1 WT 2 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R1_001.fastq.gz 18067X14_200629_A00421_0211_BHN23CDRXX_S26_L001_R2_001.fastq.gz fastq fastq 4054926360.0 39754180.0 E MTAB 13886:18067X14 200629 A00421 0211 BHN23CDRXX S26 L001 R 0:51 1:51 A:1027112898;C:978274968;G:992295226;T:1057002684;N:240584 51 51     1027112898 978274968 992295226 1057002684 240584 ERX12099016 ERS18400121 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures
15395 15395 ERR12724511 ERX12099010 ERS18400115 ERP158370 PRJEB73599 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E-MTAB-13886 Transcriptome Analysis Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted. ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29   Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold. Foxg1 het 9 E MTAB 13886:Foxg1 het 9   isolate:not applicable|organism:Danio rerio|organism:Danio rerio|collection date:not collected|scientific name:Danio rerio|common name:zebrafish|organism part:whole organism|developmental stage:pharyngula prim 5|genotype:Foxg1a het|geographic location country and/or sea:not collected                 RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings E MTAB 13886:Foxg1 het 9 p Foxg1 het 9 p RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.   RNA-Seq TRANSCRIPTOMIC Inverse rRNA PAIRED ILLUMINA Illumina NovaSeq 6000   ERP158370 Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings ENA FIRST PUBLIC:2024 03 29|ENA LAST UPDATE:2024 03 29 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R1_001.fastq.gz 18067X11_200629_A00421_0211_BHN23CDRXX_S18_L001_R2_001.fastq.gz fastq fastq 2866917570.0 28107035.0 E MTAB 13886:18067X11 200629 A00421 0211 BHN23CDRXX S18 L001 R 0:51 1:51 A:725353172;C:688761995;G:699694713;T:752936948;N:170742 51 51     725353172 688761995 699694713 752936948 170742 ERX12099010 ERS18400115 ERA29264914 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era unknown rrna_depletion trueseq bulk bulk bulk   United Kingdom 2024-03-29 Pharyngula Embryo Whole Organism All anatomical structures

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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");;