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
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
25345,SRR25868018,SRX21589435,SRS18767008,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 3,GSM7749541,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749541,GSM7749541: 20m des trunk group 3; Danio rerio; RNA Seq,GSM7749541 r1,GSM7749541,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_112_S23_L003_R1_001.fastq.gz P25101_112_S23_L003_R2_001.fastq.gz,fastq fastq,22210763348.0,73545574.0,GSM7749541 r1,0:151 1:151,A:5912051069;C:5198859790;G:5393563455;T:5706179211;N:109823,151,151,,,5912051069,5198859790,5393563455,5706179211,109823,SRX21589435,SRS18767008,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95876,0.95266,0.03675,0.03686,0.80085,0.80379,0.54105,0.54121,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25346,SRR25868019,SRX21589434,SRS18767007,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 2,GSM7749540,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749540,GSM7749540: 20m des trunk group 2; Danio rerio; RNA Seq,GSM7749540 r1,GSM7749540,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_111_S22_L003_R1_001.fastq.gz P25101_111_S22_L003_R2_001.fastq.gz,fastq fastq,28432907098.0,94148699.0,GSM7749540 r1,0:151 1:151,A:7530352460;C:6691515017;G:7032193813;T:7178705133;N:140675,151,151,,,7530352460,6691515017,7032193813,7178705133,140675,SRX21589434,SRS18767007,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95304,0.94619,0.0303,0.03073,0.81288,0.81734,0.54159,0.529,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25347,SRR25868020,SRX21589433,SRS18767006,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m des trunk group 1,GSM7749539,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,20m des trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749539,GSM7749539: 20m des trunk group 1; Danio rerio; RNA Seq,GSM7749539 r1,GSM7749539,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_110_S21_L003_R1_001.fastq.gz P25101_110_S21_L003_R2_001.fastq.gz,fastq fastq,22459067748.0,74367774.0,GSM7749539 r1,0:151 1:151,A:6073562522;C:5194312729;G:5517056007;T:5674024886;N:111604,151,151,,,6073562522,5194312729,5517056007,5674024886,111604,SRX21589433,SRS18767006,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95491,0.94862,0.03326,0.03384,0.8047,0.80949,0.54962,0.53948,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25348,SRR25868021,SRX21589432,SRS18767005,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 3,GSM7749538,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749538,GSM7749538: 20m wt trunk group 3; Danio rerio; RNA Seq,GSM7749538 r1,GSM7749538,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_109_S20_L003_R1_001.fastq.gz P25101_109_S20_L003_R2_001.fastq.gz,fastq fastq,18161226926.0,60136513.0,GSM7749538 r1,0:151 1:151,A:4953172808;C:4151930418;G:4504584090;T:4551451588;N:88022,151,151,,,4953172808,4151930418,4504584090,4551451588,88022,SRX21589432,SRS18767005,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.94707,0.93454,0.03335,0.03308,0.80127,0.80708,0.56515,0.57038,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25349,SRR25868022,SRX21589431,SRS18767004,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 2,GSM7749537,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749537,GSM7749537: 20m wt trunk group 2; Danio rerio; RNA Seq,GSM7749537 r1,GSM7749537,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_108_S19_L003_R1_001.fastq.gz P25101_108_S19_L003_R2_001.fastq.gz,fastq fastq,21168501250.0,70094375.0,GSM7749537 r1,0:151 1:151,A:5676216227;C:4922704340;G:5191762300;T:5377713558;N:104825,151,151,,,5676216227,4922704340,5191762300,5377713558,104825,SRX21589431,SRS18767004,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.95544,0.94706,0.03451,0.03439,0.80998,0.81339,0.53843,0.50395,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25350,SRR25868023,SRX21589430,SRS18767003,SRP457978,PRJNA1011839,fhl2b expression ameliorates muscular dystrophy [20 month EOM and trunk],GSE242134,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,20m wt trunk group 1,GSM7749536,,source name:20 mpf trunk muscle|age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,20m wt trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,20 mpf trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,age:20 mpf|tissue:trunk muscle|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749536,GSM7749536: 20m wt trunk group 1; Danio rerio; RNA Seq,GSM7749536 r1,GSM7749536,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457978,,loader:fastq load.py,P25101_107_S18_L003_R1_001.fastq.gz P25101_107_S18_L003_R2_001.fastq.gz,fastq fastq,21809914520.0,72218260.0,GSM7749536 r1,0:151 1:151,A:5826455436;C:5083672325;G:5302648618;T:5597031501;N:106640,151,151,,,5826455436,5083672325,5302648618,5597031501,106640,SRX21589430,SRS18767003,SRA1703875,Umeå Univeristy,Umeå Univeristy,2,0.96041,0.95117,0.03443,0.03455,0.80598,0.80872,0.50583,0.4806,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25357,SRR25868059,SRX21589476,SRS18767049,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 3,GSM7749569,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749569,GSM7749569: des trunk group 3; Danio rerio; RNA Seq,GSM7749569 r1,GSM7749569,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_112_S16_L001_R1_001.fastq.gz P17251_112_S16_L001_R2_001.fastq.gz,fastq fastq,32975158332.0,109189266.0,GSM7749569 r1,0:151 1:151,A:8971397485;C:7542039111;G:8200961544;T:8260356002;N:404190,151,151,,,8971397485,7542039111,8200961544,8260356002,404190,SRX21589476,SRS18767049,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.9452,0.93318,0.03379,0.0337,0.80586,0.81485,0.56577,0.57552,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25358,SRR25868060,SRX21589475,SRS18767048,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 2,GSM7749568,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749568,GSM7749568: des trunk group 2; Danio rerio; RNA Seq,GSM7749568 r1,GSM7749568,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_111_S15_L001_R1_001.fastq.gz P17251_111_S15_L001_R2_001.fastq.gz,fastq fastq,30771044854.0,101890877.0,GSM7749568 r1,0:151 1:151,A:8428723125;C:6962884900;G:7664589629;T:7714459134;N:388066,151,151,,,8428723125,6962884900,7664589629,7714459134,388066,SRX21589475,SRS18767048,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94539,0.80414,0.03024,0.02542,0.8464,0.86281,0.50835,0.55329,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25359,SRR25868061,SRX21589474,SRS18767045,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,des trunk group 1,GSM7749567,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / |geo loc name:missing|collection date:missing,des trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:desma / ;desmb / ,GSM7749567,GSM7749567: des trunk group 1; Danio rerio; RNA Seq,GSM7749567 r1,GSM7749567,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_110_S14_L001_R1_001.fastq.gz P17251_110_S14_L001_R2_001.fastq.gz,fastq fastq,33874542116.0,112167358.0,GSM7749567 r1,0:151 1:151,A:8845255279;C:8046911900;G:8618139910;T:8363818933;N:416094,151,151,,,8845255279,8046911900,8618139910,8363818933,416094,SRX21589474,SRS18767045,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94628,0.9369,0.02168,0.02198,0.83252,0.83816,0.5082,0.51978,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25360,SRR25868062,SRX21589473,SRS18767047,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 3,GSM7749566,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 3,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749566,GSM7749566: wt trunk group 3; Danio rerio; RNA Seq,GSM7749566 r1,GSM7749566,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_109_S13_L001_R1_001.fastq.gz P17251_109_S13_L001_R2_001.fastq.gz,fastq fastq,34282805044.0,113519222.0,GSM7749566 r1,0:151 1:151,A:9124351621;C:8034310406;G:8391950458;T:8731771604;N:420955,151,151,,,9124351621,8034310406,8391950458,8731771604,420955,SRX21589473,SRS18767047,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.95625,0.95068,0.03255,0.03282,0.80555,0.81081,0.5875,0.58319,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25361,SRR25868063,SRX21589472,SRS18767046,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 2,GSM7749565,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 2,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749565,GSM7749565: wt trunk group 2; Danio rerio; RNA Seq,GSM7749565 r1,GSM7749565,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_108_S12_L001_R1_001.fastq.gz P17251_108_S12_L001_R2_001.fastq.gz,fastq fastq,29439584536.0,97482068.0,GSM7749565 r1,0:151 1:151,A:7923205722;C:6779291710;G:7327163186;T:7409562179;N:361739,151,151,,,7923205722,6779291710,7327163186,7409562179,361739,SRX21589472,SRS18767046,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94148,0.933,0.03555,0.03563,0.80562,0.81302,0.53017,0.5746,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
25362,SRR25868064,SRX21589471,SRS18767044,SRP457980,PRJNA1011841,fhl2b expression ameliorates muscular dystrophy [5 month EOM and trunk],GSE242136,Transcriptome Analysis,In muscle dystrophies  muscle fibers loose integrity and die  leading to significant suffering and a shorter life. Strikingly  the extraocular muscles EOMs  controlling eye movements  are spared and function well despite the disease progression. Although EOMs have been shown to have important differences compared to body musculature the mechanisms underlying this inherent resistance to muscle dystrophies remain largely unknown. Here  we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscle in zebrafish via transcriptomic profiling. We show that the LIM protein Fhl2 is upregulated in response to knockout of desmin  plectin and obscurin  intermediate filament proteins causing different muscle dystrophies  and contributes to disease protection of the EOMs. Moreover  we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje  significantly improving their survival rate. Therefore  fhl2 is a protective agent and a candidate target gene for therapy of muscle dystrophies. Overall design: To examine the innate resistance of extraocular muscle to muscular dystrophies we knocked down desmin and sequenced extraocular muscle as well as trunk muscle from zebrafish at two time points. We then performed gene expression analysis between WT and desmin knock down tissues of the same type at the same time points.,parent bioproject:PRJNA1011837,pubmed:38431640,,wt trunk group 1,GSM7749564,,source name:trunk muscle|tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT|geo loc name:missing|collection date:missing,wt trunk group 1,Sequence reads were mapped to GRCz11 using STAR options:   outSAMtype BAM SortedByCoordinate   seedSearchStartLmax 12   outFilterScoreMinOverLread 0.3   alignSJoverhangMin 15   outFilterMismatchNmax 33   outFilterMatchNminOverLread 0   outFilterType BySJout   outSAMunmapped Within   outSAMattributes NH HI AS NM MD   outSAMstrandField intronMotif   quantMode GeneCounts Read count extraction and normalization were performed using R package DeSEQ2 Assembly: GRCz11 Supplementary files format and content: tab delimited text files include raw counts,trunk muscle,,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,WT AB zebrafish used originated from the same line utilized when generating the desma / ;desmb /  double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C,tissue:trunk muscle|age:5 mpf|strain:AB|cell type:Trunk muscle myofibers|genotype:WT,GSM7749564,GSM7749564: wt trunk group 1; Danio rerio; RNA Seq,GSM7749564 r1,GSM7749564,1,Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA later solution from Sigma and stored at  80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction. Illumina TruSeq Stranded mRNA  poly A selection,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP457980,,loader:fastq load.py,P17251_107_S11_L001_R1_001.fastq.gz P17251_107_S11_L001_R2_001.fastq.gz,fastq fastq,30984282826.0,102596963.0,GSM7749564 r1,0:151 1:151,A:8167387484;C:7329431316;G:7662021788;T:7825061355;N:380883,151,151,,,8167387484,7329431316,7662021788,7825061355,380883,SRX21589471,SRS18767044,SRA1703878,Umeå Univeristy,Umeå Univeristy,2,0.94444,0.93765,0.03334,0.03351,0.80089,0.80535,0.56476,0.50751,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Adult,Adult,Multi-tissue,Multi-system
26518,SRR26050763,SRX21767119,SRS18873424,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells,GSM7778660,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778660,GSM7778660: psmb1 mutants  72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778660 r1,GSM7778660,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M4_R1_001.fastq.gz sox10_M4_R2_001.fastq.gz,fastq fastq,17203316400.0,57344388.0,GSM7778660 r1,0:150 1:150,A:4557769784;C:4038080087;G:4028545423;T:4578857383;N:63723,150,150,,,4557769784,4038080087,4028545423,4578857383,63723,SRX21767119,SRS18873424,SRA1711572,BWH,BWH,2,0.93924,0.93866,0.10703,0.1068,0.70597,0.70508,0.52195,0.52023,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26519,SRR26050764,SRX21767118,SRS18873423,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells,GSM7778659,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778659,GSM7778659: psmb1 mutants  72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778659 r1,GSM7778659,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M3_R1_001.fastq.gz sox10_M3_R2_001.fastq.gz,fastq fastq,16490564400.0,54968548.0,GSM7778659 r1,0:150 1:150,A:4465032867;C:3767540674;G:3755500192;T:4502428180;N:62487,150,150,,,4465032867,3767540674,3755500192,4502428180,62487,SRX21767118,SRS18873423,SRA1711572,BWH,BWH,2,0.92805,0.92792,0.14244,0.14225,0.69639,0.69757,0.52133,0.52056,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26520,SRR26050765,SRX21767117,SRS18873422,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells,GSM7778658,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1 / ,GSM7778658,GSM7778658: psmb1 mutants  72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778658 r1,GSM7778658,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_M1_R1_001.fastq.gz sox10_M1_R2_001.fastq.gz,fastq fastq,14363136600.0,47877122.0,GSM7778658 r1,0:150 1:150,A:3843987690;C:3329370255;G:3310959116;T:3878765025;N:54514,150,150,,,3843987690,3329370255,3310959116,3878765025,54514,SRX21767117,SRS18873422,SRA1711572,BWH,BWH,2,0.92722,0.92625,0.11695,0.11644,0.69611,0.6969,0.52036,0.522,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26521,SRR26050766,SRX21767116,SRS18873421,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells,GSM7778657,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778657,GSM7778657: psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778657 r1,GSM7778657,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH4_R1_001.fastq.gz sox10_WH4_R2_001.fastq.gz,fastq fastq,14383303200.0,47944344.0,GSM7778657 r1,0:150 1:150,A:3825787510;C:3356860561;G:3322388892;T:3878211922;N:54315,150,150,,,3825787510,3356860561,3322388892,3878211922,54315,SRX21767116,SRS18873421,SRA1711572,BWH,BWH,2,0.93157,0.93024,0.09771,0.09735,0.7177,0.71829,0.52664,0.52877,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26522,SRR26050767,SRX21767115,SRS18873420,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells,GSM7778656,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778656,GSM7778656: psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778656 r1,GSM7778656,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH3_R1_001.fastq.gz sox10_WH3_R2_001.fastq.gz,fastq fastq,13772364600.0,45907882.0,GSM7778656 r1,0:150 1:150,A:3599468762;C:3277366623;G:3241941715;T:3653534992;N:52508,150,150,,,3599468762,3277366623,3241941715,3653534992,52508,SRX21767115,SRS18873420,SRA1711572,BWH,BWH,2,0.94023,0.93961,0.07684,0.07628,0.70654,0.70682,0.50963,0.51111,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26523,SRR26050768,SRX21767114,SRS18873419,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells,GSM7778655,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778655,GSM7778655: psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778655 r1,GSM7778655,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH2_R1_001.fastq.gz sox10_WH2_R2_001.fastq.gz,fastq fastq,15229813200.0,50766044.0,GSM7778655 r1,0:150 1:150,A:4029459993;C:3570808650;G:3534029380;T:4095461104;N:54073,150,150,,,4029459993,3570808650,3534029380,4095461104,54073,SRX21767114,SRS18873419,SRA1711572,BWH,BWH,2,0.93346,0.93269,0.13006,0.13022,0.70094,0.70007,0.51067,0.50945,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
26524,SRR26050769,SRX21767113,SRS18873418,SRP460207,PRJNA1016321,The proteasome subunit psmb1 is essential for craniofacial cartilage maturation and morphogenesis,GSE243072,Transcriptome Analysis,Craniofacial dysmorphisms are among the most common birth defects. Proteasome mutations frequently result in craniofacial dysmorphisms including lower jaw malformations; however  the underlying mechanisms are unknown. Here we use a zebrafish proteasome subunit beta 1 psmb1 mutant to define the cellular mechanisms underlying proteasome mutation induced craniofacial dysmorphisms. psmb1 mutants exhibit a flattened ceratohyal and smaller Meckel's and palatoquadrate cartilages. Ceratohyal flattening is a result of failed chondrocyte convergent extension  accompanied by reduced numbers of chondrocytes in the lower jaw due to defects in chondrocyte differentiation. Morphogenesis of craniofacial muscles and tendons is similarly perturbed. psmb1 mutants lack the hyohyal muscles and craniofacial tendons are shortened and disorganized. We additionally identify a critical period for proteasome function in craniofacial development  specifically during chondrocyte and muscle differentiation. psmb1 overexpression in sox10+ cells of mutant embryos rescued both cartilage and tendon phenotypes but induced only a partial rescue of the muscle phenotype  indicating that psmb1 is required in both tissue autonomous and non autonomous fashions during craniofacial development. Overall  our work demonstrates that psmb1 is required for craniofacial cartilage  tendon  and muscle differentiation and morphogenesis. Overall design: To investigate the role of psmb1 in craniofacial chondrocyte and muscle development  we sorted sox10+ cells or mylz2+ cells from the heads of psmb1 mutant zebrafish vs. pooled wild type and heterozygous larvae at 72hpf. We then performed bulk RNA sequencing and differential gene expression analysis.,,pubmed:39171526,,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells,GSM7778654,,source name:cranial sox10+ cells neural crest/chondrocytes|tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells,Reads were aligned to the GRCz11 reference assembly using STAR Dobin et al.  2013 and differential gene expression analysis was performed with DESeq2 Love et al.  2014. Assembly: GRCz11 Supplementary files format and content: text file with raw counts for each sample for sox10 samples Supplementary files format and content: text file with raw counts for each sample for mylz2 samples,cranial sox10+ cells neural crest/chondrocytes,,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,Embryos were raised in E3 at 28.5C until 72hpf.,tissue:cranial sox10+ cells neural crest/chondrocytes|genotype:psmb1+/+;+/ ,GSM7778654,GSM7778654: psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial sox10+ cells; Danio rerio; RNA Seq,GSM7778654 r1,GSM7778654,1,20 25 heads per sample were dissected from 72hpf larvae. Dissociation was carried out using 25ug/ml liberase Sigma Aldrich 05401119001  and samples were incubated on a 600rpm shaker at 37C for 30 minutes. To encourage dissociation  samples were pipetted 20 25 times every 8 10 minutes. Samples were then passed through a 40 μm filter. Cells were sorted into Buffer RLT with 1% β mercaptoethanol and RNA was isolated using the Qiagen RNeasy MicroKit Qiagen 74004. For RNA seq on sox10:kaede+ cells  7000 cells were sorted per sample. For RNA seq on mylz2+ cells  1500 cells were sorted per sample. The SMART Seq HT kit was used for full length cDNA synthesis and amplification Takara  San Jose  CA  USA  and the Illumina Nextera XT kit Illumina  San Diego  CA  USA was used for sequencing library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP460207,,loader:fastq load.py,sox10_WH1_R1_001.fastq.gz sox10_WH1_R2_001.fastq.gz,fastq fastq,13483692600.0,44945642.0,GSM7778654 r1,0:150 1:150,A:3567731759;C:3163438678;G:3137216449;T:3615254758;N:50956,150,150,,,3567731759,3163438678,3137216449,3615254758,50956,SRX21767113,SRS18873418,SRA1711572,BWH,BWH,2,0.92459,0.92408,0.11911,0.11956,0.7027,0.70264,0.50884,0.50322,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Multi-tissue,Multi-system
35871,SRR33167498,SRX28428354,SRS24751227,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2B L6.D708,GSM8919410,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2B L6.D708,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919410,GSM8919410: MB125 2B L6.D708; Danio rerio; RNA Seq,GSM8919410 r1,GSM8919410,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2B_L6.D708_1.fastq.gz MB125_2B_L6.D708_2.fastq.gz,fastq fastq,2319886164.0,22743982.0,GSM8919410 r1,0:51 1:51,A:553297266;C:587452449;G:584241025;T:594875512;N:19912,51,51,,,553297266,587452449,584241025,594875512,19912,SRX28428354,SRS24751227,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35872,SRR33167499,SRX28428353,SRS24751225,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1H L6.D705,GSM8919409,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1H L6.D705,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919409,GSM8919409: MB125 1H L6.D705; Danio rerio; RNA Seq,GSM8919409 r1,GSM8919409,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1H_L6.D705_1.fastq.gz MB125_1H_L6.D705_2.fastq.gz,fastq fastq,2373981966.0,23274333.0,GSM8919409 r1,0:51 1:51,A:568938101;C:599603085;G:595620007;T:609800208;N:20565,51,51,,,568938101,599603085,595620007,609800208,20565,SRX28428353,SRS24751225,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35873,SRR33167500,SRX28428352,SRS24751226,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1G L6.D707,GSM8919408,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1G L6.D707,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919408,GSM8919408: MB125 1G L6.D707; Danio rerio; RNA Seq,GSM8919408 r1,GSM8919408,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1G_L6.D707_1.fastq.gz MB125_1G_L6.D707_2.fastq.gz,fastq fastq,2557560036.0,25074118.0,GSM8919408 r1,0:51 1:51,A:619676841;C:640365331;G:637208159;T:660287312;N:22393,51,51,,,619676841,640365331,637208159,660287312,22393,SRX28428352,SRS24751226,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35874,SRR33167501,SRX28428351,SRS24751224,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1F L6.D706,GSM8919407,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1F L6.D706,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919407,GSM8919407: MB125 1F L6.D706; Danio rerio; RNA Seq,GSM8919407 r1,GSM8919407,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1F_L6.D706_1.fastq.gz MB125_1F_L6.D706_2.fastq.gz,fastq fastq,2646607362.0,25947131.0,GSM8919407 r1,0:51 1:51,A:620307465;C:682923030;G:678065242;T:665289569;N:22056,51,51,,,620307465,682923030,678065242,665289569,22056,SRX28428351,SRS24751224,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35875,SRR33167502,SRX28428350,SRS24751223,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1D L6.D703,GSM8919406,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1D L6.D703,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919406,GSM8919406: MB125 1D L6.D703; Danio rerio; RNA Seq,GSM8919406 r1,GSM8919406,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1D_L6.D703_1.fastq.gz MB125_1D_L6.D703_2.fastq.gz,fastq fastq,2431917150.0,23842325.0,GSM8919406 r1,0:51 1:51,A:589729741;C:608847610;G:603837645;T:629482079;N:20075,51,51,,,589729741,608847610,603837645,629482079,20075,SRX28428350,SRS24751223,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35876,SRR33167503,SRX28428349,SRS24751222,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1C L6.D704,GSM8919405,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1C L6.D704,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919405,GSM8919405: MB125 1C L6.D704; Danio rerio; RNA Seq,GSM8919405 r1,GSM8919405,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1C_L6.D704_1.fastq.gz MB125_1C_L6.D704_2.fastq.gz,fastq fastq,2525909130.0,24763815.0,GSM8919405 r1,0:51 1:51,A:624391801;C:621947668;G:618750869;T:660797379;N:21413,51,51,,,624391801,621947668,618750869,660797379,21413,SRX28428349,SRS24751222,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35877,SRR33167504,SRX28428348,SRS24751221,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 1A L6.D702,GSM8919404,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf loc name:missing|collection date:missing,MB125 1A L6.D702,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf,GSM8919404,GSM8919404: MB125 1A L6.D702; Danio rerio; RNA Seq,GSM8919404 r1,GSM8919404,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_1A_L6.D702_1.fastq.gz MB125_1A_L6.D702_2.fastq.gz,fastq fastq,2374806432.0,23282416.0,GSM8919404 r1,0:51 1:51,A:570636423;C:598720207;G:596247498;T:609181713;N:20591,51,51,,,570636423,598720207,596247498,609181713,20591,SRX28428348,SRS24751221,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35887,SRR33167514,SRX28428338,SRS24751210,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3H L7.D707,GSM8919421,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3H L7.D707,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919421,GSM8919421: MB125 3H L7.D707; Danio rerio; RNA Seq,GSM8919421 r1,GSM8919421,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3H_L7.D707_1.fastq.gz MB125_3H_L7.D707_2.fastq.gz,fastq fastq,2507284134.0,24581217.0,GSM8919421 r1,0:51 1:51,A:606166191;C:629419207;G:624900622;T:646726697;N:71417,51,51,,,606166191,629419207,624900622,646726697,71417,SRX28428338,SRS24751210,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35888,SRR33167515,SRX28428337,SRS24751211,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3G L7.D705,GSM8919420,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3G L7.D705,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919420,GSM8919420: MB125 3G L7.D705; Danio rerio; RNA Seq,GSM8919420 r1,GSM8919420,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3G_L7.D705_1.fastq.gz MB125_3G_L7.D705_2.fastq.gz,fastq fastq,2312886924.0,22675362.0,GSM8919420 r1,0:51 1:51,A:558808137;C:581346006;G:578068942;T:594600445;N:63394,51,51,,,558808137,581346006,578068942,594600445,63394,SRX28428337,SRS24751211,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35889,SRR33167516,SRX28428336,SRS24751209,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3F L7.D706,GSM8919419,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3F L7.D706,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919419,GSM8919419: MB125 3F L7.D706; Danio rerio; RNA Seq,GSM8919419 r1,GSM8919419,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3F_L7.D706_1.fastq.gz MB125_3F_L7.D706_2.fastq.gz,fastq fastq,2752811598.0,26988349.0,GSM8919419 r1,0:51 1:51,A:667499048;C:689713749;G:683954270;T:711568265;N:76266,51,51,,,667499048,689713749,683954270,711568265,76266,SRX28428336,SRS24751209,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35898,SRR33167525,SRX28428327,SRS24751200,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3C L7.D704,GSM8919418,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3C L7.D704,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919418,GSM8919418: MB125 3C L7.D704; Danio rerio; RNA Seq,GSM8919418 r1,GSM8919418,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3C_L7.D704_1.fastq.gz MB125_3C_L7.D704_2.fastq.gz,fastq fastq,2190157566.0,21472133.0,GSM8919418 r1,0:51 1:51,A:516553798;C:562413569;G:556139060;T:554989063;N:62076,51,51,,,516553798,562413569,556139060,554989063,62076,SRX28428327,SRS24751200,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35899,SRR33167526,SRX28428326,SRS24751198,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3B L7.D703,GSM8919417,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3B L7.D703,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919417,GSM8919417: MB125 3B L7.D703; Danio rerio; RNA Seq,GSM8919417 r1,GSM8919417,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3B_L7.D703_1.fastq.gz MB125_3B_L7.D703_2.fastq.gz,fastq fastq,2461970328.0,24136964.0,GSM8919417 r1,0:51 1:51,A:580053108;C:631261740;G:628153535;T:622435609;N:66336,51,51,,,580053108,631261740,628153535,622435609,66336,SRX28428326,SRS24751198,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35900,SRR33167527,SRX28428325,SRS24751199,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 3A L7.D702,GSM8919416,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1|geo loc name:missing|collection date:missing,MB125 3A L7.D702,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf colonized with microbes control|experiment:1,GSM8919416,GSM8919416: MB125 3A L7.D702; Danio rerio; RNA Seq,GSM8919416 r1,GSM8919416,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_3A_L7.D702_1.fastq.gz MB125_3A_L7.D702_2.fastq.gz,fastq fastq,2473120152.0,24246276.0,GSM8919416 r1,0:51 1:51,A:582740589;C:634217342;G:630143939;T:625950246;N:68036,51,51,,,582740589,634217342,630143939,625950246,68036,SRX28428325,SRS24751199,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Larval,Larval,Multi-tissue,Multi-system
35901,SRR33167528,SRX28428324,SRS24751197,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2H L6.D701,GSM8919415,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2H L6.D701,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919415,GSM8919415: MB125 2H L6.D701; Danio rerio; RNA Seq,GSM8919415 r1,GSM8919415,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2H_L6.D701_1.fastq.gz MB125_2H_L6.D701_2.fastq.gz,fastq fastq,2248766358.0,22046729.0,GSM8919415 r1,0:51 1:51,A:535472034;C:572268414;G:569258495;T:571751143;N:16272,51,51,,,535472034,572268414,569258495,571751143,16272,SRX28428324,SRS24751197,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35902,SRR33167529,SRX28428323,SRS24751196,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2G L6.D711,GSM8919414,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2G L6.D711,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919414,GSM8919414: MB125 2G L6.D711; Danio rerio; RNA Seq,GSM8919414 r1,GSM8919414,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2G_L6.D711_1.fastq.gz MB125_2G_L6.D711_2.fastq.gz,fastq fastq,2198049510.0,21549505.0,GSM8919414 r1,0:51 1:51,A:535878049;C:547290891;G:544359481;T:570502976;N:18113,51,51,,,535878049,547290891,544359481,570502976,18113,SRX28428323,SRS24751196,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35903,SRR33167530,SRX28428322,SRS24751195,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2F L6.D712,GSM8919413,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2F L6.D712,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919413,GSM8919413: MB125 2F L6.D712; Danio rerio; RNA Seq,GSM8919413 r1,GSM8919413,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2F_L6.D712_1.fastq.gz MB125_2F_L6.D712_2.fastq.gz,fastq fastq,2601840378.0,25508239.0,GSM8919413 r1,0:51 1:51,A:584354104;C:693159013;G:696042575;T:628262140;N:22546,51,51,,,584354104,693159013,696042575,628262140,22546,SRX28428322,SRS24751195,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35904,SRR33167531,SRX28428321,SRS24751194,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2E L6.D709,GSM8919412,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2E L6.D709,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919412,GSM8919412: MB125 2E L6.D709; Danio rerio; RNA Seq,GSM8919412 r1,GSM8919412,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2E_L6.D709_1.fastq.gz MB125_2E_L6.D709_2.fastq.gz,fastq fastq,2393568822.0,23466361.0,GSM8919412 r1,0:51 1:51,A:573394367;C:604936257;G:602232683;T:612984188;N:21327,51,51,,,573394367,604936257,602232683,612984188,21327,SRX28428321,SRS24751194,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
35905,SRR33167532,SRX28428320,SRS24751192,SRP579141,PRJNA1251588,Investigation into molecular mechanisms behind microbiome and normal neurobehavioral development in zebrafish,GSE294778,Transcriptome Analysis,Changes in resident microbiota may have wide ranging effects on human health. Previous research found axenic zebrafish Danio rerio exhibit hyperactivity at 10 dpf dpf. This abnormal neurobehavioral response can be prevented with re colonization of axenic embryos with microbes at 1 dpf. The present study investigated the molecular mechanism behind this effect through RNA sequencing of pooled 10 dpf larval head tissue from axenic  conventionally colonized controls  and axenic zebrafish recolonized with microbes at 1 dpf. Overall design: 10 dpf dpf axenic microbe free  conventionally colonized normal  and axenic Danio rerio embryos recolonized with microbes at 1 dpf control for axenic derivation process were submitted for RNA sequencing to investigate the molecular mechanism behind hyperactivity in axenic larvae.,,,,MB125 2D L6.D710,GSM8919411,,source name:pooled heads collected anterior to swim bladder of larval zebrafish|tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1|geo loc name:missing|collection date:missing,MB125 2D L6.D710,For Experiment 1  basecall files were converted to FASTQ by bcl2fastq2  demultiplexed  quality trimmed  and filter using ea utils https://expressionanalysis.github.io/ea utils/ ; last accessed 01 21 2020. Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed. For Experiment 2  Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed  respectively in Partek Flow v.8.0.19.0428; St. Louis  MO. Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR v.2.5.3a with default settings in Partek Flow and strand specificity detection enabled for the paired end reads from Experiment 1 but not for Experiment 2. Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation. Assembly: GRCz11/93 gene annotation Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples,pooled heads collected anterior to swim bladder of larval zebrafish,,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,tissue:pooled heads collected anterior to swim bladder of larval zebrafish|strain:mixed wild type zebrafish line US EPA|lifestage:larvae|age:10 dpf re colonized with microbes on day 1|experiment:1,GSM8919411,GSM8919411: MB125 2D L6.D710; Danio rerio; RNA Seq,GSM8919411 r1,GSM8919411,1,Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis  LLC Morrisville  NC  USA. Samples from experiment 2 underwent RNA extraction at US EPA Durham  NC  USA using Direct zol™ RNA MiniPrep Plus kit Zymo Research per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit. For Experiment 1  paired end 50 base pair total RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo Zero Gold Library Prep Kit for rRNA depletion Illumina  San Diego  California  cat. No. RS 1222303 at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly  rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer DNA 1000 kit #5067 1504 and qPCR KAPA Library Quant Kit #KK4824  KAPA Biosystems  Wilmington  MA. Sample libraries were then normalized  randomly pooled  and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2  purified RNA from each sample 500 ng per sample were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA Durham  NC  USA. PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product's quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size bp was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library μl x nM was pooled from 16 randomized libraries to make the sequencing samples total 2 pools of 16 libraries each and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR Single Read.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP579141,,,MB125_2D_L6.D710_1.fastq.gz MB125_2D_L6.D710_2.fastq.gz,fastq fastq,2322596610.0,22770555.0,GSM8919411 r1,0:51 1:51,A:563147167;C:580081508;G:578201930;T:601145790;N:20215,51,51,,,563147167,580081508,578201930,601145790,20215,SRX28428320,SRS24751192,SRA2113523,US EPA,US EPA,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2025-04-16,Multi-stage,Multi-stage,Multi-tissue,Multi-system
55673,SRR10721218,SRX7397865,SRS5845643,SRP237948,PRJNA596232,RNA sequencing of zebrafish asxl1+/+ and asxl1 / ,GSE142214,Transcriptome Analysis,ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients  ASXL1 mutations are usually heterozygous frameshift or non sense mutations leading to C terminal truncation. Here  we generated an endogenous C terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage  neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants  we performed RNA seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed  the expression of neutrophil markers were all included in down regulated genes. Nonetheless  the expression of myeloid progenitor marker and macrophage marker  were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated post mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore  transcriptome analysis mainly represented the disruption of neutrophil development. Overall design: 3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp,,pubmed:33483612,,asxl1 MUT B,GSM4222803,,tissue:3dpf embryo's tail|Stage:3dpf|genotype:asxl1 / ,asxl1 MUT B,The reads were mapped onto the GRCz11 zebrafish reference genome  using STAR Dobin et al.  2013. Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts Liao et al.  2014 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include feature counts for each Sample,3dpf embryo's tail,No treatments were applied prior to RNA extraction,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described Kimmel et al.  1995. The mutants were based on an AB background.,Stage:3dpf|genotype:asxl1 / ,GSM4222803,GSM4222803: asxl1 MUT B; Danio rerio; RNA Seq,GSM4222803,,1,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,GEO Accession:GSM4222803,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP237948,,,asxl1_MUT_B_1.fq.gz asxl1_MUT_B_2.fq.gz,fastq fastq,8539660200.0,28465534.0,GSM4222803 r1,0:150 1:150,A:2250292446;C:2015024018;G:2096676101;T:2177532680;N:134955,150,150,,,2250292446,2015024018,2096676101,2177532680,134955,SRX7397865,SRS5845643,SRA1013371,GEO,"Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology",2,0.9519,0.95085,0.07684,0.07685,0.71135,0.7138,0.43808,0.44748,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,China,2019-12-17,Larval,Larval,Tail,Multi-system
55674,SRR10721217,SRX7397864,SRS5845642,SRP237948,PRJNA596232,RNA sequencing of zebrafish asxl1+/+ and asxl1 / ,GSE142214,Transcriptome Analysis,ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients  ASXL1 mutations are usually heterozygous frameshift or non sense mutations leading to C terminal truncation. Here  we generated an endogenous C terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage  neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants  we performed RNA seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed  the expression of neutrophil markers were all included in down regulated genes. Nonetheless  the expression of myeloid progenitor marker and macrophage marker  were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated post mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore  transcriptome analysis mainly represented the disruption of neutrophil development. Overall design: 3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp,,pubmed:33483612,,asxl1 MUT A,GSM4222802,,tissue:3dpf embryo's tail|Stage:3dpf|genotype:asxl1 / ,asxl1 MUT A,The reads were mapped onto the GRCz11 zebrafish reference genome  using STAR Dobin et al.  2013. Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts Liao et al.  2014 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include feature counts for each Sample,3dpf embryo's tail,No treatments were applied prior to RNA extraction,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described Kimmel et al.  1995. The mutants were based on an AB background.,Stage:3dpf|genotype:asxl1 / ,GSM4222802,GSM4222802: asxl1 MUT A; Danio rerio; RNA Seq,GSM4222802,,1,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,GEO Accession:GSM4222802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP237948,,,asxl1_MUT_A_2.fq.gz asxl1_MUT_A_1.fq.gz,fastq fastq,8373503700.0,27911679.0,GSM4222802 r1,0:150 1:150,A:2195102709;C:1988209021;G:2071316288;T:2118740981;N:134701,150,150,,,2195102709,1988209021,2071316288,2118740981,134701,SRX7397864,SRS5845642,SRA1013371,GEO,"Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology",2,0.95365,0.95278,0.07501,0.07475,0.70859,0.70981,0.4432,0.43808,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,China,2019-12-17,Larval,Larval,Tail,Multi-system
55675,SRR10721216,SRX7397863,SRS5845641,SRP237948,PRJNA596232,RNA sequencing of zebrafish asxl1+/+ and asxl1 / ,GSE142214,Transcriptome Analysis,ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients  ASXL1 mutations are usually heterozygous frameshift or non sense mutations leading to C terminal truncation. Here  we generated an endogenous C terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage  neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants  we performed RNA seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed  the expression of neutrophil markers were all included in down regulated genes. Nonetheless  the expression of myeloid progenitor marker and macrophage marker  were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated post mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore  transcriptome analysis mainly represented the disruption of neutrophil development. Overall design: 3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp,,pubmed:33483612,,asxl1 WT B,GSM4222801,,tissue:3dpf embryo's tail|Stage:3dpf|genotype:asxl1+/+,asxl1 WT B,The reads were mapped onto the GRCz11 zebrafish reference genome  using STAR Dobin et al.  2013. Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts Liao et al.  2014 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include feature counts for each Sample,3dpf embryo's tail,No treatments were applied prior to RNA extraction,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described Kimmel et al.  1995. The mutants were based on an AB background.,Stage:3dpf|genotype:asxl1+/+,GSM4222801,GSM4222801: asxl1 WT B; Danio rerio; RNA Seq,GSM4222801,,1,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,GEO Accession:GSM4222801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP237948,,,asxl1_WT_B_2.fq.gz asxl1_WT_B_1.fq.gz,fastq fastq,11172785400.0,37242618.0,GSM4222801 r1,0:150 1:150,A:2949987819;C:2635154635;G:2744703802;T:2842759006;N:180138,150,150,,,2949987819,2635154635,2744703802,2842759006,180138,SRX7397863,SRS5845641,SRA1013371,GEO,"Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology",2,0.95222,0.95038,0.07973,0.07953,0.70877,0.71206,0.44092,0.43989,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,China,2019-12-17,Larval,Larval,Tail,Multi-system
55676,SRR10721215,SRX7397862,SRS5845640,SRP237948,PRJNA596232,RNA sequencing of zebrafish asxl1+/+ and asxl1 / ,GSE142214,Transcriptome Analysis,ASXL1 gene is one of the most frequently mutated genes in malignant myeloid diseases. In patients  ASXL1 mutations are usually heterozygous frameshift or non sense mutations leading to C terminal truncation. Here  we generated an endogenous C terminal truncated Asxl1 mutant in zebrafish which is more comparable to human malignant leukemia patients. Our data showed that at embryonic stage  neutrophil differentiation was explicitly blocked in our mutant. To understand the basis for the impairment of neutrophil differentiation in zebrafish asxl1 mutants  we performed RNA seq of asxl1 mutants at 3dpf and their littermate controls. Similar with the phenotype we observed  the expression of neutrophil markers were all included in down regulated genes. Nonetheless  the expression of myeloid progenitor marker and macrophage marker  were not impaired in asxl1 mutants. We also found inflammatory cytokine and matrix metalloproteinases were upregulated post mutated asxl1. It suggests that neutrophil deficiency may stimulate the expression of some inflammatory cytokines and enhances the inflammatory responds. Therefore  transcriptome analysis mainly represented the disruption of neutrophil development. Overall design: 3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit. Sequencing was done on an Illumina NovaSeq sequencing platform to obtain 150bp 2 ´ 150 bp,,pubmed:33483612,,asxl1 WT A,GSM4222800,,tissue:3dpf embryo's tail|Stage:3dpf|genotype:asxl1+/+,asxl1 WT A,The reads were mapped onto the GRCz11 zebrafish reference genome  using STAR Dobin et al.  2013. Raw read counts were for each gene were calculated with Ensembl annotation by Featurecounts Liao et al.  2014 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include feature counts for each Sample,3dpf embryo's tail,No treatments were applied prior to RNA extraction,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,Zebrafish were raised and maintained under standard conditions. Embryos were raised at 28.5°C and incubated in “egg water” containing 0.002% methylene blue as a fungicide. Embryos were collected and morphologically staged as described Kimmel et al.  1995. The mutants were based on an AB background.,Stage:3dpf|genotype:asxl1+/+,GSM4222800,GSM4222800: asxl1 WT A; Danio rerio; RNA Seq,GSM4222800,,1,3 dpf dpf asxl1+/+ and asxl1 /  embryos from asxl1+/  intercross were collected and extract total RNA from the tails including CHT. Each sample is a pool of tails about 20. RNA was extracted using TRIzol Invitrogen. Sequencing libraries were prepared from total RNA using Novogene NGS RNA Library Prep Kit.,GEO Accession:GSM4222800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP237948,,,asxl1_WT_A_2.fq.gz asxl1_WT_A_1.fq.gz,fastq fastq,9741478500.0,32471595.0,GSM4222800 r1,0:150 1:150,A:2552181418;C:2313499814;G:2411847512;T:2463815584;N:134172,150,150,,,2552181418,2313499814,2411847512,2463815584,134172,SRX7397862,SRS5845640,SRA1013371,GEO,"Laboratory of Developmental Biology and Regenerative Medicine, School of Medicine, South China University of Technology",2,0.9537,0.95279,0.07341,0.07332,0.71104,0.71149,0.42841,0.42847,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,China,2019-12-17,Larval,Larval,Tail,Multi-system
59847,SRR12045011,SRX8573981,SRS6865979,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Y1 positive rep3,GSM4625932,,tissue:non venous endothelial  blood  and arch mesenchyme|Stage:38 hpf isolated cells,Y1 positive rep3,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,non venous endothelial  blood  and arch mesenchyme,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625932,GSM4625932: Y1 positive rep3; Danio rerio; RNA Seq,GSM4625932,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625932,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,y1_WT3.R1.fastq y1_WT3.R2.fastq,fastq fastq,5234292300.0,52342923.0,GSM4625932 r1,0:50 1:50,A:1227937371;C:1289958798;G:1435480505;T:1278798354;N:2117272,50,50,,,1227937371,1289958798,1435480505,1278798354,2117272,SRX8573981,SRS6865979,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.82522,0.83953,0.3086,0.32178,0.76656,0.76719,0.70833,0.52608,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Multi-tissue,Multi-system
59848,SRR12045010,SRX8573980,SRS6865978,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Y1 positive rep2,GSM4625931,,tissue:non venous endothelial  blood  and arch mesenchyme|Stage:38 hpf isolated cells,Y1 positive rep2,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,non venous endothelial  blood  and arch mesenchyme,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625931,GSM4625931: Y1 positive rep2; Danio rerio; RNA Seq,GSM4625931,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625931,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,y1_WT2.R1.fastq y1_WT2.R2.fastq,fastq fastq,4819929000.0,48199290.0,GSM4625931 r1,0:50 1:50,A:1127729164;C:1190781602;G:1322881210;T:1176579941;N:1957083,50,50,,,1127729164,1190781602,1322881210,1176579941,1957083,SRX8573980,SRS6865978,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.82508,0.83939,0.30667,0.31875,0.76607,0.76601,0.71058,0.50542,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Multi-tissue,Multi-system
59849,SRR12045009,SRX8573979,SRS6865976,SRP267842,PRJNA640350,Bulk RNA seq data to assess an improved zebrafish transcriptome annotation,GSE152759,Transcriptome Analysis,oligo dT and random primed RNA seq libraries were used to test an improved annotation of the zebrafish transcriptome Overall design: RNA seq was performed on transgene positive cells isolated by FACS,,pubmed:32831172,,Y1 positive rep1,GSM4625930,,tissue:non venous endothelial  blood  and arch mesenchyme|Stage:38 hpf isolated cells,Y1 positive rep1,Raw HiSeq2000 data files were processed with CASAVA 1.8.2 Illumina to generate fastq files for inserts and index sequences. Demultiplexing of index sequences was done with CASAVA. For both samples  if index sequences were non redundant  we allowed for 1 mismatch or N in the index. Paired end reads were mapped to the zebrafish genome GRCz11 using STAR Mapped reads were quantified using Ensembl v95  RefSeq GCF 000002035.6  or a custom annotation V4.3.gtf  included as processed file using RSEM Differentially expressed genes were identified using DEseq2 RNAseq pipeline was run in the DolphinNext environment Genome build: GRz11 Supplementary files format and content: CSV formatted output from DEseq2 for differential gene expression and normalized expression values quantified with 3 different annotations; GTF file for customized V4.3 annotation,non venous endothelial  blood  and arch mesenchyme,embryos were dissociated into single cell suspensions  immunostained with Nr2fantibody and secondary fluorescent tagged antibody; EGFP and Nr2f2 positive cells were isolated by fluorescence activated cell sorting.,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,,Stage:38 hpf isolated cells,GSM4625930,GSM4625930: Y1 positive rep1; Danio rerio; RNA Seq,GSM4625930,,1,total RNA was treated with Ribogone and libraries constructed using the SMARTer Stranded RNA Seq Kit Clontech,GEO Accession:GSM4625930,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP267842,,,y1_WT1.R1.fastq y1_WT1.R2.fastq,fastq fastq,5013318600.0,50133186.0,GSM4625930 r1,0:50 1:50,A:1107366794;C:1303452559;G:1450795494;T:1149648426;N:2055327,50,50,,,1107366794,1303452559,1450795494,1149648426,2055327,SRX8573979,SRS6865976,SRA1088645,GEO,"Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School",2,0.84299,0.85327,0.23393,0.24314,0.76396,0.76572,0.71204,0.56072,50,50,B,B,biological fallback assumption,illumina,hiseq_era,full_length,poly_a,smarter,bulk,bulk,bulk,,United States,2020-06-18,Pharyngula,Embryo,Multi-tissue,Multi-system
66032,SRR15831122,SRX12122768,SRS10102627,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 4,GSM5571381,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571381,GSM5571381: WTCR 4; Danio rerio; RNA Seq,GSM5571381,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571381,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_4_WT_S4_L001_R1_001.fastq.gz 110_4_WT_S4_L001_R2_001.fastq.gz,fastq fastq,4329797898.0,42448999.0,GSM5571381 r1,0:51 1:51,A:1091279009;C:1032920355;G:1051132020;T:1149383481;N:5083033,51,51,,,1091279009,1032920355,1051132020,1149383481,5083033,SRX12122768,SRS10102627,SRA1290854,GEO,Duke University School of Medicine,2,0.95402,0.96397,0.08543,0.07562,0.73217,0.73089,0.5458,0.55389,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66033,SRR15831123,SRX12122768,SRS10102627,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 4,GSM5571381,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 4,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571381,GSM5571381: WTCR 4; Danio rerio; RNA Seq,GSM5571381,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571381,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_4_WT_S4_L002_R1_001.fastq.gz 110_4_WT_S4_L002_R2_001.fastq.gz,fastq fastq,4418873988.0,43322294.0,GSM5571381 r2,0:51 1:51,A:1112718386;C:1055462529;G:1072853555;T:1175023364;N:2816154,51,51,,,1112718386,1055462529,1072853555,1175023364,2816154,SRX12122768,SRS10102627,SRA1290854,GEO,Duke University School of Medicine,2,0.96205,0.96538,0.0864,0.07712,0.73255,0.73121,0.5531,0.55124,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66034,SRR15831120,SRX12122767,SRS10102626,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 3,GSM5571380,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571380,GSM5571380: WTCR 3; Danio rerio; RNA Seq,GSM5571380,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571380,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_3_WT_S3_L001_R1_001.fastq.gz 110_3_WT_S3_L001_R2_001.fastq.gz,fastq fastq,4220050080.0,41373040.0,GSM5571380 r1,0:51 1:51,A:1066697606;C:1018843395;G:1010678417;T:1118873112;N:4957550,51,51,,,1066697606,1018843395,1010678417,1118873112,4957550,SRX12122767,SRS10102626,SRA1290854,GEO,Duke University School of Medicine,2,0.95486,0.966,0.07043,0.06386,0.73596,0.73521,0.55591,0.55878,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66035,SRR15831121,SRX12122767,SRS10102626,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 3,GSM5571380,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 3,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571380,GSM5571380: WTCR 3; Danio rerio; RNA Seq,GSM5571380,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571380,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_3_WT_S3_L002_R1_001.fastq.gz 110_3_WT_S3_L002_R2_001.fastq.gz,fastq fastq,4333573224.0,42486012.0,GSM5571380 r2,0:51 1:51,A:1094639610;C:1047853818;G:1037481119;T:1150831500;N:2767177,51,51,,,1094639610,1047853818,1037481119,1150831500,2767177,SRX12122767,SRS10102626,SRA1290854,GEO,Duke University School of Medicine,2,0.96356,0.96864,0.07004,0.06331,0.73484,0.73442,0.55192,0.55245,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66036,SRR15831118,SRX12122766,SRS10102625,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 2,GSM5571379,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571379,GSM5571379: WTCR 2; Danio rerio; RNA Seq,GSM5571379,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571379,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_2_WT_S2_L001_R1_001.fastq.gz 110_2_WT_S2_L001_R2_001.fastq.gz,fastq fastq,5185225896.0,50835548.0,GSM5571379 r1,0:51 1:51,A:1304070987;C:1258911045;G:1261604762;T:1354546875;N:6092227,51,51,,,1304070987,1258911045,1261604762,1354546875,6092227,SRX12122766,SRS10102625,SRA1290854,GEO,Duke University School of Medicine,2,0.95818,0.96692,0.06611,0.06155,0.72788,0.72721,0.55376,0.54209,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66037,SRR15831119,SRX12122766,SRS10102625,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 2,GSM5571379,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 2,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571379,GSM5571379: WTCR 2; Danio rerio; RNA Seq,GSM5571379,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571379,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_2_WT_S2_L002_R1_001.fastq.gz 110_2_WT_S2_L002_R2_001.fastq.gz,fastq fastq,5276889420.0,51734210.0,GSM5571379 r2,0:51 1:51,A:1326273057;C:1282893223;G:1283803668;T:1380588152;N:3331320,51,51,,,1326273057,1282893223,1283803668,1380588152,3331320,SRX12122766,SRS10102625,SRA1290854,GEO,Duke University School of Medicine,2,0.96598,0.9679,0.06636,0.06169,0.72663,0.72679,0.54857,0.54885,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66038,SRR15831116,SRX12122765,SRS10102624,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 1,GSM5571378,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571378,GSM5571378: WTCR 1; Danio rerio; RNA Seq,GSM5571378,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571378,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_1_WT_S1_L001_R1_001.fastq.gz 110_1_WT_S1_L001_R2_001.fastq.gz,fastq fastq,3886947354.0,38107327.0,GSM5571378 r1,0:51 1:51,A:977212071;C:945237801;G:942123031;T:1017804127;N:4570324,51,51,,,977212071,945237801,942123031,1017804127,4570324,SRX12122765,SRS10102624,SRA1290854,GEO,Duke University School of Medicine,2,0.95964,0.96709,0.06425,0.06051,0.72837,0.72732,0.55884,0.55071,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system
66039,SRR15831117,SRX12122765,SRS10102624,SRP336372,PRJNA762031,Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response,GSE183799,Transcriptome Analysis,The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g /  zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type  hnf4g /   and hnf4a / ;hnf4g /   zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts  and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV  WTGF  hnf4g / CV  hnf4g / GF 2 WTCR  hnf4g / CR  hnf4a / ;hnf4g / CR,,pubmed:36218393,,WTCR 1,GSM5571378,,source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,WTCR 1,Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar,dissected GI tract,,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,,tissue:dissected GI tract|genotype:wild type|microbial status:Conventionally rasied|age:6 dpf,GSM5571378,GSM5571378: WTCR 1; Danio rerio; RNA Seq,GSM5571378,,1,larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols,GEO Accession:GSM5571378,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP336372,,loader:fastq load.py,110_1_WT_S1_L002_R1_001.fastq.gz 110_1_WT_S1_L002_R2_001.fastq.gz,fastq fastq,3989187972.0,39109686.0,GSM5571378 r2,0:51 1:51,A:1002352842;C:971622035;G:966544703;T:1046123663;N:2544729,51,51,,,1002352842,971622035,966544703,1046123663,2544729,SRX12122765,SRS10102624,SRA1290854,GEO,Duke University School of Medicine,2,0.96634,0.96887,0.06453,0.06085,0.72947,0.72932,0.55939,0.53599,51,51,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-09-09,Larval,Larval,Multi-tissue,Multi-system