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
9702,ERR3301003,ERX3327070,ERS3389658,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 3,SAMEA5585434,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585434|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:6|organism part:heart|sample name:E MTAB 7920:WT heart rep 3|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 3 p,WT heart rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart3_2.fq.gz,fastq fastq,7339830080.0,45873938.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart3 ,0:80 1:80,A:1985328994;C:1673818891;G:1695753386;T:1984031668;N:897141,80,80,,,1985328994,1673818891,1695753386,1984031668,897141,ERX3327070,ERS3389658,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.9311,0.94858,0.07774,0.07789,0.76378,0.76394,0.52815,0.52065,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9703,ERR3301002,ERX3327069,ERS3389657,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 2,SAMEA5585433,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585433|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:5|organism part:heart|sample name:E MTAB 7920:WT heart rep 2|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 2 p,WT heart rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart2_2.fq.gz,fastq fastq,7486415840.0,46790099.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart2 ,0:80 1:80,A:2020798219;C:1702752807;G:1731176796;T:2030756525;N:931493,80,80,,,2020798219,1702752807,1731176796,2030756525,931493,ERX3327069,ERS3389657,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93397,0.9509,0.07752,0.07859,0.76019,0.76002,0.54034,0.54728,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9704,ERR3301001,ERX3327068,ERS3389656,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,WT heart rep 1,SAMEA5585432,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585432|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:normal|genotype:wild type genotype|individual:4|organism part:heart|sample name:E MTAB 7920:WT heart rep 1|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT heart rep 1 p,WT heart rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:wild type genotype|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTheart1_2.fq.gz,fastq fastq,6814600800.0,42591255.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTheart1 ,0:80 1:80,A:1823108307;C:1567497576;G:1587567005;T:1835589927;N:837985,80,80,,,1823108307,1567497576,1587567005,1835589927,837985,ERX3327068,ERS3389656,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93109,0.94806,0.07581,0.07635,0.75907,0.75988,0.54746,0.54753,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9708,ERR3300997,ERX3327064,ERS3389652,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 3,SAMEA5585428,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585428|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 3|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:3|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 3|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 3 p,Mutant heart rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart3_2.fq.gz,fastq fastq,7240447520.0,45252797.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart3 ,0:80 1:80,A:1968283412;C:1645458614;G:1652590010;T:1973242527;N:872957,80,80,,,1968283412,1645458614,1652590010,1973242527,872957,ERX3327064,ERS3389652,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.92784,0.94597,0.08601,0.08686,0.76702,0.76449,0.50929,0.52685,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9709,ERR3300996,ERX3327063,ERS3389651,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 2,SAMEA5585427,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585427|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 2|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:2|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 2|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 2 p,Mutant heart rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart2_2.fq.gz,fastq fastq,7347029600.0,45918935.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart2 ,0:80 1:80,A:1967915665;C:1690507331;G:1712776156;T:1974918219;N:912229,80,80,,,1967915665,1690507331,1712776156,1974918219,912229,ERX3327063,ERS3389651,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93337,0.94978,0.07673,0.07724,0.76755,0.76798,0.53415,0.51157,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9710,ERR3300995,ERX3327062,ERS3389650,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Mutant heart rep 1,SAMEA5585426,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:02Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585426|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:02Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant heart rep 1|age:1|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|disease:Naxos disease|genotype:sa12692 mutant|individual:1|organism part:heart|sample name:E MTAB 7920:Mutant heart rep 1|scientific name:Danio rerio|sex:female|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant heart rep 1 p,Mutant heart rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Each adult fish was euthanized using MS 222 and secured ventral side up in a Petri dish. A micro scissors was used to make an incision from the base of one pectoral fin to the other. A second incision was made from the centre of the first incision to the gill area. Fine needles were used to pin back the chest wall and expose the heart. The ventricle  atrium and bulbus arteriosus were located. The bulbus arteriosus was cut to detach it from the gills. The entire intact heart was removed by pinching the bulbus arteriosus with a forceps and making one final cut between the atrium and sinus venosus. For RNA extractions  hearts were rinsed in sterile PBS and stored in RNAlater® until use. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples were incubated at  80°C for 30 minutes followed by centrifugation at 18000 g for 30 minutes. The isopropanol was discarded and 200 µL of ice cold ethanol was added to wash the pellet. The samples were centrifuged for a final 5 minutes at 18000 g. The ethanol was discarded and the pellets were air dried for 5 10 minutes. The samples were resuspended in 20 µL nuclease free water. The RNA was stored at  80°C. The quality/integrity of the RNA was assessed with the use of an Agilent RNA 6000 nano kit on an Agilent Bioanalyzer 2100  by following the manufacturer's instructions. RNA integrity was measured by a software tool on the Agilent Bioanalyzer which calculates an RNA integrity number RIN for each sample. Only RINs ≥8 were accepted for library synthesis. RNA concentration and purity was assessed on a Qubit Fluorometer using the Qubit® RNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. The values obtained for RNA concentration were used to calculate the amount needed for the library preparation. Total RNA was converted to a cDNA library using the Illumina TruSeq® Stranded mRNA Library Preparation Kit  following the manufacturer's instructions. An RNA input of 1000 ng was used for larval samples and 600 ng for adult heart samples. The only minor but important deviation from the protocol was a shorter drying time for the magnetic beads due to the temperature of the lab environment. The recommended drying time of 15 minutes was reduced to 10 minutes. Briefly  the polyA containing mRNA molecules were purified and fragmented into smaller pieces. First strand cDNA was synthesised from the cleaved RNA fragments using reverse transcriptase and random primers. The RNA fragments were removed and double stranded cDNA was synthesised with the incorporation of dUTP instead of dTTP in the second strand. Strand specificity was achieved by degradation of the second strand as the polymerase used does not recognise past the dUTP nucleotide. The three prime ends of the cDNA fragments were adenylated to prevent them ligating to each other. Complementary indexing adapters were ligated to the ends of the fragments to allow hybridisation of the fragments to the flow cell at the sequencing stage. A final PCR step ensured enrichment of cDNA fragments with adapters at both ends and amplification of the library. The size and purity of each library sample was assessed on an Agilent Bioanalyzer using the Agilent DNA 1000 Kit. The DNA of each library sample was quantified on a Qubit Fluorometer using the Qubit dsDNA HS High Sensitivity Assay Kit  according to the manufacturer's instructions. All 12 samples were pooled at equal concentration and the quality of the final product was validated on an Agilent Bioanalyzer. The average fragment size was 270 bp.,Experimental Factor: genotype:sa12692 mutant|Experimental Factor: developmental stage:adult|Experimental Factor: organism part:heart,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantheart1_2.fq.gz,fastq fastq,6296502880.0,39353143.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantheart1 ,0:80 1:80,A:1677737687;C:1460767489;G:1468915029;T:1688319734;N:762941,80,80,,,1677737687,1460767489,1468915029,1688319734,762941,ERX3327062,ERS3389650,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93775,0.9516,0.07994,0.08077,0.75844,0.75759,0.51937,0.52207,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Adult,Adult,Multi-tissue,Multi-system
9812,ERR3931362,ERX3938952,ERS4329529,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 ED,SAMEA6565186,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565186|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 ED s,WKM 7 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,10_WKM_7_ED.fastq.gz,fastq,3603783627.0,47724788.0,E MTAB 8800:WKM 7 ED,0:75.51 1:0,A:730277817;C:1059558661;G:1006087781;T:807771859;N:87509,75,0,,,730277817,1059558661,1006087781,807771859,87509,ERX3938952,ERS4329529,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96114,,0.20335,,0.83798,,0.76524,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9813,ERR3931361,ERX3938951,ERS4329528,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 7 EaD,SAMEA6565185,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565185|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 7 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM7|organism part:head kidney|sample name:E MTAB 8800:WKM 7 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 7 EaD s,WKM 7 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,11_WKM_7_EaD_1.fastq.gz,fastq,3127207407.0,41417754.0,E MTAB 8800:WKM 7 EaD,0:75.50 1:0,A:618290483;C:948661192;G:891134088;T:669046822;N:74822,75,0,,,618290483,948661192,891134088,669046822,74822,ERX3938951,ERS4329528,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96441,,0.20171,,0.85427,,0.75425,,76,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9814,ERR3931360,ERX3938950,ERS4329527,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 ED,SAMEA6565184,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565184|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 ED|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 ED,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 ED s,WKM 5 ED s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:n1,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,8_WKM_5_ED.fastq.gz,fastq,3762435507.0,49825705.0,E MTAB 8800:WKM 5 ED,0:75.51 1:0,A:760573477;C:1107794761;G:1060998015;T:832975681;N:93573,75,0,,,760573477,1107794761,1060998015,832975681,93573,ERX3938950,ERS4329527,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96233,,0.20628,,0.84141,,0.73601,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
9815,ERR3931359,ERX3938949,ERS4329526,ERP120057,PRJEB36819,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E-MTAB-8800,Transcriptome Analysis,Kit ligand Kitlg is a pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Due to whole genome duplication  zebrafish possess two copies of Kit ligand Kitlga and Kitlgb. We generated a recombinant version of Kitlga  tested its biological activity in culture of zebrafish kidney marrow cells and performed RNA seq analysis. Using this assay  we demonstrate that Kitlga cooperates with other factors to promote erythroid cell expansion ex vivo.,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,,Protocols: Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,WKM 5 EaD,SAMEA6565183,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 12 31|ENA last update:2021 12 31|External Id:SAMEA6565183|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 12 31T00:11:11Z|INSDC last update:2021 12 31T00:11:11Z|INSDC status:public|Submitter Id:E MTAB 8800:WKM 5 EaD|broker name:ArrayExpress|cell type:erythroid progenitor cell|common name:zebrafish|developmental stage:adult|disease:normal|genotype:Tg gata1:DsRed|growth condition:Erythropoietin  Dexamethas1|individual:WKM5|organism part:head kidney|sample name:E MTAB 8800:WKM 5 EaD,,,,,,,,,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,E MTAB 8800:WKM 5 EaD s,WKM 5 EaD s,Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,Zebrafish whole kidney marrow WKM cells were isolated as described in Svoboda  O. et al. Ex vivo tools for the clonal analysis of zebrafish hematopoiesis. Nature protocols 11  1007 1020  doi:10.1038/nprot.2016.053 2016. Total RNA was isolated from 6 7×10 6 WKM cells cultivated in the presence of erythropoietin Epo  dexamethasone Dex or Epo  Dex and Kitlga  according to the PureLink Micro Kit Invitrogen manufacturer's protocol that includes DNase I treatment. The quantity of isolated RNA was measured spectrophotometrically using NanoDrop ND 1000 Thermo Fisher Scientific and its quality was analyzed by Agilent 2100 Bioanalyser Agilent Technologies. RNA integrity number  which is regarded as criteria for high quality total RNA  ranged between 9.5 and 10. Takara SMARTer Stranded Total RNA Seq Kit v2 Takara Bio was used for cDNAlibrary preparation starting with 3.5 ng of total RNA. Library size distribution was evaluated on the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit Agilent Technologies.,Experimental Factor: stimulus:kit ligand,RNA-Seq,TRANSCRIPTOMIC,Inverse rRNA,SINGLE,ILLUMINA,NextSeq 500,,ERP120057,NextSeq 500 sequencing; Transcription profiling by RNA seq of zebrafish kidney marrow cells treated with Kitlga,ENA FIRST PUBLIC:2022 01 05|ENA LAST UPDATE:2022 01 05,9_WKM_5_EaD.fastq.gz,fastq,3602342027.0,47707938.0,E MTAB 8800:WKM 5 EaD,0:75.51 1:0,A:717278291;C:1084375347;G:1027250408;T:773351695;N:86286,75,0,,,717278291,1084375347,1027250408,773351695,86286,ERX3938949,ERS4329526,ERA2383450,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.96461,,0.20281,,0.85303,,0.74553,,75,,B,,usable mapping rate,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,bulk,bulk,,Czech Republic,2021-12-31,Adult,Adult,Multi-tissue,Multi-system
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
24582,SRR25462250,SRX21195051,SRS18453977,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 3,GSM7669027,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669027,GSM7669027: PG HE 8mpf 3; Danio rerio; RNA Seq,GSM7669027 r1,GSM7669027,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_3_S11_L003_R1_001.fastq.gz HE_PG_8mpf_3_S11_L003_R2_001.fastq.gz,fastq fastq,7161373434.0,60309247.0,GSM7669027 r1,0:59.39 1:59.35,A:1783731260;C:1744025029;G:1733970346;T:1880173306;N:19473493,59,59,,,1783731260,1744025029,1733970346,1880173306,19473493,SRX21195051,SRS18453977,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94187,0.94592,0.01475,0.01464,0.77447,0.77498,0.45855,0.4635,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24583,SRR25462251,SRX21195050,SRS18453976,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 2,GSM7669026,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669026,GSM7669026: PG HE 8mpf 2; Danio rerio; RNA Seq,GSM7669026 r1,GSM7669026,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_2_S7_L003_R1_001.fastq.gz HE_PG_8mpf_2_S7_L003_R2_001.fastq.gz,fastq fastq,3176994053.0,26828357.0,GSM7669026 r1,0:59.22 1:59.20,A:793619267;C:767135191;G:764404567;T:830643823;N:21191205,59,59,,,793619267,767135191,764404567,830643823,21191205,SRX21195050,SRS18453976,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.93822,0.94226,0.01596,0.0161,0.77684,0.77772,0.47008,0.46904,59,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24584,SRR25462252,SRX21195049,SRS18453975,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG HE 8mpf 1,GSM7669025,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ |geo loc name:missing|collection date:missing,PG HE 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:HE cdkn1a +/ ,GSM7669025,GSM7669025: PG HE 8mpf 1; Danio rerio; RNA Seq,GSM7669025 r1,GSM7669025,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,HE_PG_8mpf_1_S6_L003_R1_001.fastq.gz HE_PG_8mpf_1_S6_L003_R2_001.fastq.gz,fastq fastq,4587580737.0,38590260.0,GSM7669025 r1,0:59.45 1:59.43,A:1149031944;C:1121086335;G:1106925902;T:1203970839;N:6565717,59,59,,,1149031944,1121086335,1106925902,1203970839,6565717,SRX21195049,SRS18453975,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94032,0.9437,0.01481,0.01462,0.77682,0.77774,0.45843,0.4699,58,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24585,SRR25462253,SRX21195048,SRS18453974,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 3,GSM7669024,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 3,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669024,GSM7669024: PG WT 8mpf 3; Danio rerio; RNA Seq,GSM7669024 r1,GSM7669024,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_3_S8_L003_R2_001.fastq.gz WT_PG_8mpf_3_S8_L003_R1_001.fastq.gz,fastq fastq,3920821867.0,33089226.0,GSM7669024 r1,0:59.26 1:59.23,A:977738236;C:951999354;G:944769809;T:1023828622;N:22485846,59,59,,,977738236,951999354,944769809,1023828622,22485846,SRX21195048,SRS18453974,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94193,0.94555,0.01657,0.01646,0.76784,0.76919,0.47238,0.47016,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24586,SRR25462254,SRX21195047,SRS18453973,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 2,GSM7669023,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 2,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669023,GSM7669023: PG WT 8mpf 2; Danio rerio; RNA Seq,GSM7669023 r1,GSM7669023,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_2_S10_L003_R2_001.fastq.gz WT_PG_8mpf_2_S10_L003_R1_001.fastq.gz,fastq fastq,4917868553.0,41430484.0,GSM7669023 r1,0:59.37 1:59.33,A:1231173294;C:1195692797;G:1182545852;T:1292018757;N:16437853,59,59,,,1231173294,1195692797,1182545852,1292018757,16437853,SRX21195047,SRS18453973,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94048,0.94432,0.0178,0.0178,0.75645,0.7569,0.46332,0.46812,59,57,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
24587,SRR25462255,SRX21195046,SRS18453972,SRP452270,PRJNA1000445,CDKN1A Deficiency in Zebrafish Promote Follicle Maturation and Degeneration Mediated by CRISPR/Cas9 Targeted Disruption,GSE239622,Transcriptome Analysis,CDKN1A plays multiple roles in distinctive biological processes  such as cellular proliferation  apoptosis  DNA repairing  and etc. In mouse  Cdkn1a deficiency led to cell arrest at G1 phase  and also reported that Cdkna1 deficient mice were susceptible to tumorigenesis. However  the functions of Cdkn1a in zebrafish were still elusive due to few studies. Our previous study indicated that Cdkn1a might be closely associated with folliculogenesis  and to further investigate its specific role during folliculogenesis  Cdkn1a was targeted disrupted by CRISPR/Cas9. Interestingly  Cdkn1a deficient zebrafish were embryonic lethality  resulted in approximate 2% homozygous mutants in adult stage. Furthermore  homozygous mutants have accelerated follicle maturation that faster than WT  and were fertile at young age 2 month. However  the matured or large follicles in mutant soon become dysfunctional due to abnormal oocyte that led to infertile at 3 month. Gradually  the abnormal follicles were undertaken follicle degeneration  resulted in PG follicle enrichment in mutant ovary at 6 month. Similar follicle degeneration phenomenon was also observed in heterozygous mutant ovary at 8 month. The degenerating follicles in mutant were convinced by in situ apoptosis detection kit. To further explore molecular mechanism  RNA seq and qPCR validation were adopted to identify underlying molecular pathway that involved in Cdkn1a deficient apoptosis. This study firstly reported the functions of Cdkn1a in zebrafish  particular in its critical role in maintenance of normal follicle development  and the special phenotypes in folliculogenesis perfectly interpretation of its dual roles on both proliferation and apoptosis at two different phases  which replenished its novel role in folliculogenesis that expanded our insights. Overall design: Considering Cdkn1a homozygous mutants are embryonically lethal  we use heterozygous mutants for experiments. We isolated primary folliicles PGs from both early 50 dpf dpf and 8 mpf mpf for both the WT Cdkn1+/+ and Cdkn1a +/  zebrafish. We then established bulk RNAseq libraries according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. post libraries preparation  we performed sequencing using the Genomics  Bioinformatics and Single Cell Analysis Core at the Univerisity of Macau.,,,,PG WT 8mpf 1,GSM7669022,,source name:follicle|strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+|geo loc name:missing|collection date:missing,PG WT 8mpf 1,Illumina HiSeq sequencer raw data was demultiplexed using bcl2fastq2 Quality of the sequencing data was checked using FastQC v0.11.5. No trimming was performed as the quality of data was good and there were no adapters enriched in the reads. Reads were aligned to Zebrafish genome version GRCz11 from Ensemble using HiSat2 Stringtie was used to estimate transcript level counts. Bioconductor package tximport was used to import the gene level read counts from StringTie output files. This raw counts data was analyzed for differential gene expression using DESeq2 package. Assembly: GRCz11 Supplementary files format and content: Raw read counts in a TAB delimited file Supplementary files format and content: DESeq2 normalized read counts in a TAB delimited file,follicle,,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,strain:AB|tissue:follicle|developmental stage:primary growth|age:8mpf|genotype:WT cdkn1a +/+,GSM7669022,GSM7669022: PG WT 8mpf 1; Danio rerio; RNA Seq,GSM7669022 r1,GSM7669022,1,TRIzol reagent for RNA extraction NEBNext Ultra II Directional RNA Library Prep Kit for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP452270,,,WT_PG_8mpf_1_S9_L003_R1_001.fastq.gz WT_PG_8mpf_1_S9_L003_R2_001.fastq.gz,fastq fastq,3375380667.0,28408784.0,GSM7669022 r1,0:59.42 1:59.40,A:842316103;C:825987175;G:818715765;T:881225528;N:7136096,59,59,,,842316103,825987175,818715765,881225528,7136096,SRX21195046,SRS18453972,,,"Karp 12006A, Biology of Vascular Program, Boston Children's Hospital",2,0.94039,0.9444,0.0162,0.01617,0.7697,0.76986,0.47132,0.46938,60,60,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,United States,2023-07-31,Adult,Adult,Gonad,Reproductive System
25135,SRR25649156,SRX21375305,SRS18618397,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X8,18689X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X8_R1.fastq.gz 18689X8_R2.fastq.gz,fastq fastq,8163984120.0,27033060.0,18689X8 R1.fastq.gz,0:151 1:151,A:1900143724;C:2183735704;G:2147710753;T:1932229591;N:164348,151,151,,,1900143724,2183735704,2147710753,1932229591,164348,SRX21375305,SRS18618397,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89288,0.89479,0.20193,0.20116,0.79072,0.79352,0.57246,0.56409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25136,SRR25649157,SRX21375304,SRS18618396,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X15,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X15,19629X15,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X15_R2.fastq.gz 19629X15_R1.fastq.gz,fastq fastq,10277997106.0,34033103.0,19629X15 R1.fastq.gz,0:151 1:151,A:2798108841;C:2341310321;G:2438634645;T:2699729301;N:213998,151,151,,,2798108841,2341310321,2438634645,2699729301,213998,SRX21375304,SRS18618396,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90655,0.90714,0.18082,0.18027,0.72803,0.72953,0.45722,0.45335,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25137,SRR25649158,SRX21375303,SRS18618395,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X14,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 3|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X14,19629X14,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X14_R1.fastq.gz 19629X14_R2.fastq.gz,fastq fastq,10921707086.0,36164593.0,19629X14 R1.fastq.gz,0:151 1:151,A:2969229092;C:2484790148;G:2595052715;T:2872407360;N:227771,151,151,,,2969229092,2484790148,2595052715,2872407360,227771,SRX21375303,SRS18618395,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90015,0.90211,0.19548,0.19546,0.72997,0.73131,0.53978,0.54998,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25138,SRR25649159,SRX21375302,SRS18618394,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X13,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 3|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X13,19629X13,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X13_R1.fastq.gz 19629X13_R2.fastq.gz,fastq fastq,10019262230.0,33176365.0,19629X13 R1.fastq.gz,0:151 1:151,A:2732766602;C:2270429150;G:2391166434;T:2624690350;N:209694,151,151,,,2732766602,2270429150,2391166434,2624690350,209694,SRX21375302,SRS18618394,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90381,0.90536,0.18425,0.18388,0.72681,0.72936,0.48627,0.49398,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25139,SRR25649160,SRX21375301,SRS18618393,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X12,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X12,19629X12,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X12_R1.fastq.gz 19629X12_R2.fastq.gz,fastq fastq,11078632326.0,36684213.0,19629X12 R1.fastq.gz,0:151 1:151,A:2995473302;C:2550446088;G:2653594689;T:2878887522;N:230725,151,151,,,2995473302,2550446088,2653594689,2878887522,230725,SRX21375301,SRS18618393,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91101,0.91121,0.16145,0.16142,0.70274,0.70498,0.47852,0.48788,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25140,SRR25649161,SRX21375300,SRS18618392,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X11,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X11,19629X11,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X11_R1.fastq.gz 19629X11_R2.fastq.gz,fastq fastq,10957183630.0,36282065.0,19629X11 R1.fastq.gz,0:151 1:151,A:2987773085;C:2485587980;G:2603747193;T:2879845340;N:230032,151,151,,,2987773085,2485587980,2603747193,2879845340,230032,SRX21375300,SRS18618392,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91198,0.91301,0.20992,0.20926,0.73044,0.73316,0.44301,0.43596,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25141,SRR25649162,SRX21375299,SRS18618390,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X10,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:female|tissue:intestine|isolation source:pet trade 2|replicate:E1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X10,19629X10,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X10_R1.fastq.gz 19629X10_R2.fastq.gz,fastq fastq,9549065142.0,31619421.0,19629X10 R1.fastq.gz,0:151 1:151,A:2603092155;C:2167963952;G:2264536965;T:2513273275;N:198795,151,151,,,2603092155,2167963952,2264536965,2513273275,198795,SRX21375299,SRS18618390,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.92549,0.92615,0.16176,0.15925,0.7683,0.76926,0.3093,0.30927,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25142,SRR25649163,SRX21375298,SRS18618391,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X4,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X4,18843X4,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X4_R1.fastq.gz 18843X4_R2.fastq.gz,fastq fastq,7982656072.0,26432636.0,18843X4 R1.fastq.gz,0:151 1:151,A:2135066517;C:1863182314;G:1988885981;T:1995395692;N:125568,151,151,,,2135066517,1863182314,1988885981,1995395692,125568,SRX21375298,SRS18618391,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.86144,0.85982,0.30956,0.30838,0.70731,0.71356,0.48481,0.48054,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25143,SRR25649164,SRX21375297,SRS18618389,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X5,18843X5,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X5_R1.fastq.gz 18843X5_R2.fastq.gz,fastq fastq,11487744176.0,38038888.0,18843X5 R1.fastq.gz,0:151 1:151,A:3214900282;C:2532228300;G:2651065167;T:3089370892;N:179535,151,151,,,3214900282,2532228300,2651065167,3089370892,179535,SRX21375297,SRS18618389,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91483,0.91311,0.35213,0.35037,0.68347,0.68826,0.49832,0.49905,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25144,SRR25649165,SRX21375296,SRS18618388,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X6,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X6,18843X6,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X6_R1.fastq.gz 18843X6_R2.fastq.gz,fastq fastq,8690806510.0,28777505.0,18843X6 R1.fastq.gz,0:151 1:151,A:2346658651;C:2002583855;G:2108507319;T:2232918222;N:138463,151,151,,,2346658651,2002583855,2108507319,2232918222,138463,SRX21375296,SRS18618388,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91741,0.91785,0.21796,0.21778,0.6971,0.70102,0.49123,0.51016,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25145,SRR25649166,SRX21375295,SRS18618387,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X9,18689X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X9_R1.fastq.gz 18689X9_R2.fastq.gz,fastq fastq,9420964292.0,31195246.0,18689X9 R1.fastq.gz,0:151 1:151,A:2315675361;C:2390479538;G:2363596017;T:2351024167;N:189209,151,151,,,2315675361,2390479538,2363596017,2351024167,189209,SRX21375295,SRS18618387,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87883,0.87875,0.25078,0.24834,0.75394,0.75418,0.60036,0.59504,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25146,SRR25649167,SRX21375294,SRS18618386,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X2,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X2,18843X2,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X2_R2.fastq.gz 18843X2_R1.fastq.gz,fastq fastq,8319888298.0,27549299.0,18843X2 R1.fastq.gz,0:151 1:151,A:2316006657;C:1846379220;G:1965504688;T:2191867233;N:130500,151,151,,,2316006657,1846379220,1965504688,2191867233,130500,SRX21375294,SRS18618386,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90304,0.30055,0.3001,0.68345,0.6901,0.49306,0.48285,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25147,SRR25649168,SRX21375293,SRS18618385,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X3,18843X3,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X3_R1.fastq.gz 18843X3_R2.fastq.gz,fastq fastq,9351018676.0,30963638.0,18843X3 R1.fastq.gz,0:151 1:151,A:2555870224;C:2133006230;G:2246501165;T:2415491618;N:149439,151,151,,,2555870224,2133006230,2246501165,2415491618,149439,SRX21375293,SRS18618385,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91594,0.91512,0.21678,0.21621,0.72719,0.73117,0.52961,0.53327,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25148,SRR25649169,SRX21375292,SRS18618384,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X1,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X1,18843X1,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X1_R1.fastq.gz 18843X1_R2.fastq.gz,fastq fastq,8760175608.0,29007204.0,18843X1 R1.fastq.gz,0:151 1:151,A:2335440655;C:2073187411;G:2210813716;T:2140593603;N:140223,151,151,,,2335440655,2073187411,2210813716,2140593603,140223,SRX21375292,SRS18618384,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.84641,0.8437,0.21898,0.21841,0.71301,0.72044,0.48661,0.49029,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25149,SRR25649170,SRX21375291,SRS18618383,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X9,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X9,19629X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X9_R1.fastq.gz 19629X9_R2.fastq.gz,fastq fastq,12342730940.0,40869970.0,19629X9 R1.fastq.gz,0:151 1:151,A:3339874828;C:2828928610;G:2945452577;T:3228218292;N:256633,151,151,,,3339874828,2828928610,2945452577,3228218292,256633,SRX21375291,SRS18618383,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90738,0.8127,0.19825,0.17409,0.73385,0.74659,0.54306,0.55304,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25150,SRR25649171,SRX21375290,SRS18618382,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X1,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X1,18689X1,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X1_R1.fastq.gz 18689X1_R2.fastq.gz,fastq fastq,7723999112.0,25576156.0,18689X1 R1.fastq.gz,0:151 1:151,A:1938376895;C:1923902263;G:1896332244;T:1965229370;N:158340,151,151,,,1938376895,1923902263,1896332244,1965229370,158340,SRX21375290,SRS18618382,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87233,0.87262,0.28456,0.28071,0.73858,0.7414,0.60785,0.61428,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25151,SRR25649172,SRX21375289,SRS18618381,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X5,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab cohoused|replicate:CHM1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X5,18689X5,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X5_R1.fastq.gz 18689X5_R2.fastq.gz,fastq fastq,8136028886.0,26940493.0,18689X5 R1.fastq.gz,0:151 1:151,A:2015403368;C:2051480513;G:2023331135;T:2045661742;N:152128,151,151,,,2015403368,2051480513,2023331135,2045661742,152128,SRX21375289,SRS18618381,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88067,0.88216,0.24575,0.2425,0.75018,0.75073,0.59361,0.61451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25152,SRR25649173,SRX21375288,SRS18618380,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X11,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X11,18689X11,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X11_R1.fastq.gz 18689X11_R2.fastq.gz,fastq fastq,9515677834.0,31508867.0,18689X11 R1.fastq.gz,0:151 1:151,A:2274021342;C:2477750132;G:2454285243;T:2309429465;N:191652,151,151,,,2274021342,2477750132,2454285243,2309429465,191652,SRX21375288,SRS18618380,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87714,0.87737,0.2476,0.24538,0.77968,0.78248,0.63108,0.65333,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25153,SRR25649174,SRX21375287,SRS18618379,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X8,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X8,18843X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X8_R1.fastq.gz 18843X8_R2.fastq.gz,fastq fastq,7615135964.0,25215682.0,18843X8 R1.fastq.gz,0:151 1:151,A:2157897532;C:1663478819;G:1764954395;T:2028683751;N:121467,151,151,,,2157897532,1663478819,1764954395,2028683751,121467,SRX21375287,SRS18618379,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.91455,0.91333,0.34885,0.34782,0.69467,0.70167,0.50339,0.51371,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25154,SRR25649175,SRX21375286,SRS18618378,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X9,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X9,18843X9,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X9_R1.fastq.gz 18843X9_R2.fastq.gz,fastq fastq,8819654206.0,29204153.0,18843X9 R1.fastq.gz,0:151 1:151,A:2383706177;C:2044504407;G:2140881818;T:2250422256;N:139548,151,151,,,2383706177,2044504407,2140881818,2250422256,139548,SRX21375286,SRS18618378,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.90385,0.90437,0.21274,0.21235,0.72604,0.73164,0.52888,0.52909,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25155,SRR25649176,SRX21375285,SRS18618377,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18843X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:spleen|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18843X7,18843X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18843X7_R1.fastq.gz 18843X7_R2.fastq.gz,fastq fastq,9614914732.0,31837466.0,18843X7 R1.fastq.gz,0:151 1:151,A:2577032258;C:2236946505;G:2389573431;T:2411211222;N:151316,151,151,,,2577032258,2236946505,2389573431,2411211222,151316,SRX21375285,SRS18618377,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.8913,0.88909,0.31019,0.30978,0.71721,0.72557,0.50815,0.52261,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25156,SRR25649177,SRX21375284,SRS18618376,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X3,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X3,18689X3,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X3_R1.fastq.gz 18689X3_R2.fastq.gz,fastq fastq,8819353112.0,29203156.0,18689X3 R1.fastq.gz,0:151 1:151,A:2342877591;C:2071139579;G:2035896879;T:2369259787;N:179276,151,151,,,2342877591,2071139579,2035896879,2369259787,179276,SRX21375284,SRS18618376,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.85514,0.85429,0.35095,0.34608,0.72985,0.73077,0.51131,0.53375,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25157,SRR25649178,SRX21375283,SRS18618375,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X7,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:lab|replicate:CNTM2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X7,18689X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X7_R1.fastq.gz 18689X7_R2.fastq.gz,fastq fastq,8986035368.0,29755084.0,18689X7 R1.fastq.gz,0:151 1:151,A:2169723143;C:2326462981;G:2292317481;T:2197350043;N:181720,151,151,,,2169723143,2326462981,2292317481,2197350043,181720,SRX21375283,SRS18618375,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.89254,0.89285,0.22562,0.22356,0.74911,0.75089,0.6409,0.65585,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25158,SRR25649179,SRX21375282,SRS18618374,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X12,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:spleen|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X12,18689X12,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X12_R1.fastq.gz 18689X12_R2.fastq.gz,fastq fastq,9338495642.0,30922171.0,18689X12 R1.fastq.gz,0:151 1:151,A:2151902218;C:2516218122;G:2484485366;T:2185704377;N:185559,151,151,,,2151902218,2516218122,2484485366,2185704377,185559,SRX21375282,SRS18618374,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88601,0.8889,0.17526,0.17449,0.81702,0.81801,0.46118,0.46609,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Spleen,Hematopoietic System
25159,SRR25649180,SRX21375281,SRS18618373,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,18689X4,,strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:female|tissue:kidney|isolation source:lab|replicate:CNTF1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,18689X4,18689X4,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,18689X4_R1.fastq.gz 18689X4_R2.fastq.gz,fastq fastq,9931670150.0,32886325.0,18689X4 R1.fastq.gz,0:151 1:151,A:2494588549;C:2471174839;G:2445771402;T:2519940959;N:194401,151,151,,,2494588549,2471174839,2445771402,2519940959,194401,SRX21375281,SRS18618373,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.87391,0.87402,0.31383,0.30879,0.73789,0.74014,0.63365,0.63903,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Kidney,Renal System
25160,SRR25649181,SRX21375280,SRS18618372,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X8,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X8,19629X8,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X8_R2.fastq.gz 19629X8_R1.fastq.gz,fastq fastq,10758135430.0,35622965.0,19629X8 R1.fastq.gz,0:151 1:151,A:2991372806;C:2398155523;G:2517276916;T:2851104238;N:225947,151,151,,,2991372806,2398155523,2517276916,2851104238,225947,SRX21375280,SRS18618372,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.88839,0.89055,0.23357,0.23344,0.72592,0.72851,0.53343,0.53081,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25161,SRR25649182,SRX21375279,SRS18618371,SRP455253,PRJNA1005695,Metagenomic survey of zebrafish from the laboratory and the pet trade,PRJNA1005695,Other,This study involved sequencing of bulk ribo depleted RNA from intestine  kidney  and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.,,,,,19629X7,,strain:unknown|dev stage:adult|collection date:2022 03 15|geo loc name:USA: Salt Lake City UT|sex:male|tissue:intestine|isolation source:pet trade 1|replicate:P1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of adult Danio rerio from laboratory and pet trade sources,19629X7,19629X7,Fish were sacrificed and intestines  whole kidney marrows  and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction  samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample,,,RNA-Seq,METATRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP455253,,,19629X7_R1.fastq.gz 19629X7_R2.fastq.gz,fastq fastq,11738178884.0,38868142.0,19629X7 R1.fastq.gz,0:151 1:151,A:3192358555;C:2674045852;G:2784070515;T:3087458659;N:245303,151,151,,,3192358555,2674045852,2784070515,3087458659,245303,SRX21375279,SRS18618371,SRA1693347,University of Utah|Quantitative Cell Science,University of Utah,2,0.9074,0.90829,0.20853,0.20916,0.74115,0.74369,0.53704,0.55385,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,trueseq,bulk,bulk,bulk,,United States,2023-08-15,Adult,Adult,Gut,Digestive System
25196,SRR25685540,SRX21410747,SRS18649229,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 4,GSM7717538,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 4,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717538,GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq,GSM7717538 r1,GSM7717538,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L001_OE4_cbc.fastq.gz,fastq,373009260.0,6216821.0,GSM7717538 r1,0:60,A:154344754;C:67291339;G:55785796;T:95519920;N:67451,60,,,,154344754,67291339,55785796,95519920,67451,SRX21410747,SRS18649229,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.89552,,0.06993,,0.9276,,0.58138,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25197,SRR25685541,SRX21410747,SRS18649229,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 4,GSM7717538,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 4,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717538,GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq,GSM7717538 r1,GSM7717538,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L002_OE4_cbc.fastq.gz,fastq,362301060.0,6038351.0,GSM7717538 r2,0:60,A:106180158;C:75387781;G:73886850;T:106761396;N:84875,60,,,,106180158,75387781,73886850,106761396,84875,SRX21410747,SRS18649229,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.89159,,0.06701,,0.87081,,0.62237,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25198,SRR25685542,SRX21410747,SRS18649229,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 4,GSM7717538,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 4,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717538,GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq,GSM7717538 r1,GSM7717538,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L003_OE4_cbc.fastq.gz,fastq,384538200.0,6408970.0,GSM7717538 r3,0:60,A:113163070;C:80510291;G:76775008;T:114062728;N:27103,60,,,,113163070,80510291,76775008,114062728,27103,SRX21410747,SRS18649229,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.90032,,0.06985,,0.87008,,0.61631,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25199,SRR25685543,SRX21410747,SRS18649229,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 4,GSM7717538,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 4,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717538,GSM7717538: Hmga1a overexpression sample 4; Danio rerio; RNA Seq,GSM7717538 r1,GSM7717538,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L004_OE4_cbc.fastq.gz,fastq,369674700.0,6161245.0,GSM7717538 r4,0:60,A:108130666;C:76988468;G:75491768;T:109027980;N:35818,60,,,,108130666,76988468,75491768,109027980,35818,SRX21410747,SRS18649229,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.89622,,0.06895,,0.86854,,0.61464,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25200,SRR25685544,SRX21410746,SRS18649228,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 3,GSM7717537,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 3,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717537,GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq,GSM7717537 r1,GSM7717537,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L001_OE3_cbc.fastq.gz,fastq,172977180.0,2882953.0,GSM7717537 r1,0:60,A:75387211;C:31808233;G:24071421;T:41679068;N:31247,60,,,,75387211,31808233,24071421,41679068,31247,SRX21410746,SRS18649228,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.88458,,0.06987,,0.92788,,0.58263,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25201,SRR25685545,SRX21410746,SRS18649228,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 3,GSM7717537,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 3,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717537,GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq,GSM7717537 r1,GSM7717537,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L002_OE3_cbc.fastq.gz,fastq,168370020.0,2806167.0,GSM7717537 r2,0:60,A:49447288;C:35622124;G:34182575;T:49078813;N:39220,60,,,,49447288,35622124,34182575,49078813,39220,SRX21410746,SRS18649228,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.88366,,0.06639,,0.87519,,0.43134,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25202,SRR25685546,SRX21410746,SRS18649228,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 3,GSM7717537,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 3,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717537,GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq,GSM7717537 r1,GSM7717537,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L003_OE3_cbc.fastq.gz,fastq,177341340.0,2955689.0,GSM7717537 r3,0:60,A:52304623;C:37759158;G:35264433;T:52000964;N:12162,60,,,,52304623,37759158,35264433,52000964,12162,SRX21410746,SRS18649228,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.8907,,0.06795,,0.87405,,0.57596,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25203,SRR25685547,SRX21410746,SRS18649228,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 3,GSM7717537,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 3,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717537,GSM7717537: Hmga1a overexpression sample 3; Danio rerio; RNA Seq,GSM7717537 r1,GSM7717537,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L004_OE3_cbc.fastq.gz,fastq,172482600.0,2874710.0,GSM7717537 r4,0:60,A:50610545;C:36521080;G:35043934;T:50291237;N:15804,60,,,,50610545,36521080,35043934,50291237,15804,SRX21410746,SRS18649228,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.88558,,0.06686,,0.87373,,0.57425,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System
25204,SRR25685548,SRX21410745,SRS18649227,SRP455779,PRJNA1006658,Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [bulk RNAseq Hmga1a OE],GSE241157,Transcriptome Analysis,The prospect of repairing the heart post a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish  amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species  the molecular mechanisms driving cardiomyocyte cell cycle re entry remain insufficiently understood. In this study  we employed spatial transcriptomics and identified high mobility group AT hook 1a Hmga1a as being upregulated in cardiomyocytes of the injury border zone in zebrafish  but not in mice. Through knock out and cardiomyocyte specific overexpression of hmga1a  we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition  a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically  Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally regulated genes and induced a border zone like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac xxx post injury. Overall design: TOMOseq was performed on mouse and zebrafish hearts at 3  7 and 14 xxx post injury for the interspecies comparison. single cell RNA sequencing was performed on wildtype versus hmga1a mutant zebrafish cardiomyocytes 7 days post cryoinjury to assess differences during heart regeneration. Bulk RNA sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect in an uninjured heart. bulk sortChIC sequencing was performed on control versus Hmga1a overexpression cardiomyocytes to assess the effect of Hmga1a on the chromatin.,parent bioproject:PRJNA1006653,pubmed:39747457,,Hmga1a overexpression sample 2,GSM7717536,,source name:adult heart|tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen|geo loc name:missing|collection date:missing,Hmga1a overexpression sample 2,FASTQ files were mapped with the STARandGO pipeline https://github.com/anna alemany/VASAseq/blob/main/mapping/map star.sh against the danRer11 ENSEMBL genome with the zebrafish Lawson V4.3.2 annotation. Normalization and downstream analysis were performed in R. Due to low read count  samples control 2 and overexpression 1 were excluded from analysis. Using the R package EdgeR  differentially expressed genes were obtained FC < 1 or >1 and Pval<0.05. Gene lists were subjected to GO analysis using the online tool DAVID. Assembly: danrer11 Supplementary files format and content: excel file containing edgeR results and GO analysis results Supplementary files format and content: count table spliced transcriptcounts,adult heart,zebrafish were treated with tamoxifen to induce Hmga1a overexpression,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,tissue:adult heart|genotype 1:cmlc2:dsred|genotype 2:Hmga1a overexpression|cell type:cardiomyocytes|treatment:14 days post tamoxifen,GSM7717536,GSM7717536: Hmga1a overexpression sample 2; Danio rerio; RNA Seq,GSM7717536 r1,GSM7717536,1,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP455779,,,HUB-PN-b004_HHHK2BGXN_S1_L001_OE2_cbc.fastq.gz,fastq,420273960.0,7004566.0,GSM7717536 r1,0:60,A:172608345;C:77102289;G:65053968;T:105434207;N:75151,60,,,,172608345,77102289,65053968,105434207,75151,SRX21410745,SRS18649227,SRA1695358,"Jeroen Bakkers, Hubrecht Institute","Jeroen Bakkers, Hubrecht Institute",1,0.90654,,0.06306,,0.92904,,0.38886,,60,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,Netherlands,2023-08-18,Adult,Adult,Heart,Cardiovascular System