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
9699,ERR3301006,ERX3327073,ERS3389661,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 3,SAMEA5585437,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585437|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 3|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 3 p,WT embryo rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo3_2.fq.gz,fastq fastq,7308473280.0,45677958.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo3 ,0:80 1:80,A:1898812783;C:1731426486;G:1757309247;T:1920031807;N:892957,80,80,,,1898812783,1731426486,1757309247,1920031807,892957,ERX3327073,ERS3389661,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94288,0.95671,0.07985,0.08023,0.67915,0.67815,0.47781,0.48461,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9700,ERR3301005,ERX3327072,ERS3389660,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 2,SAMEA5585436,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585436|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 2|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 2 p,WT embryo rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo2_2.fq.gz,fastq fastq,7424396000.0,46402475.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo2 ,0:80 1:80,A:1940921070;C:1754354124;G:1768688429;T:1959515088;N:917289,80,80,,,1940921070,1754354124,1768688429,1959515088,917289,ERX3327072,ERS3389660,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94222,0.95663,0.0909,0.09022,0.67929,0.67606,0.48763,0.48719,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9701,ERR3301004,ERX3327071,ERS3389659,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 1,SAMEA5585435,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585435|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:WT embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:normal|genotype:wild type genotype|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:WT embryo rep 1|scientific name:Danio rerio|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:WT embryo rep 1 p,WT embryo rep  1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1WTembryo1_2.fq.gz,fastq fastq,7300913760.0,45630711.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1WTembryo1 ,0:80 1:80,A:1931507380;C:1703881934;G:1712942848;T:1951676424;N:905174,80,80,,,1931507380,1703881934,1712942848,1951676424,905174,ERX3327071,ERS3389659,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93831,0.95401,0.09471,0.09526,0.67576,0.67403,0.48092,0.48297,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9705,ERR3301000,ERX3327067,ERS3389655,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 3,SAMEA5585431,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:47Z|External Id:SAMEA5585431|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:47Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 3|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 3 p,Mutant embryo rep 3 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo3_2.fq.gz,fastq fastq,6323854560.0,39524091.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo3 ,0:80 1:80,A:1662088892;C:1473777430;G:1500364334;T:1686853051;N:770853,80,80,,,1662088892,1473777430,1500364334,1686853051,770853,ERX3327067,ERS3389655,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93548,0.95404,0.09034,0.09103,0.67584,0.67592,0.47892,0.48193,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9706,ERR3300999,ERX3327066,ERS3389654,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 2,SAMEA5585430,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585430|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 2|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 2 p,Mutant embryo rep 2 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo2_2.fq.gz,fastq fastq,6564227680.0,41026423.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo2 ,0:80 1:80,A:1702331829;C:1557343680;G:1583770440;T:1719974488;N:807243,80,80,,,1702331829,1557343680,1583770440,1719974488,807243,ERX3327066,ERS3389654,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.94141,0.95836,0.07518,0.07501,0.67982,0.67803,0.47895,0.47763,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
9707,ERR3300998,ERX3327065,ERS3389653,ERP115040,PRJEB32363,RNA seq of zebrafish sa12692 mutants against WT controls,E-MTAB-7920,Transcriptome Analysis,Arrhythmogenic Right Ventricular Cardiomyopathy is a congenital heart disorder characterized by fibrofatty replacement of the myocardium. The exact molecular mechanisms underlying the disease remain to be elucidated and treatment options are limited. The sa12692 mutant line contains a splice site mutation in the plakoglobin gene  resulting in the expression of a truncated protein. This protein is highly similar to the protein expressed in Naxos disease  a recessive form of ARVC. RNA seq was used to investigate the effect of the sa12692 mutation on gene expression in order to uncover signalling pathways involved in the pathogenesis of ARVC. Gene expression was examined in whole larvae at 5 dpf and in hearts of 1 year old adult fish. Larvae at 5 dpf were selected as this timepoint is equivalent to birth in humans. Adult hearts were selected as ARVC is a disorder of the heart and cardiac symptoms generally manifest in maturity. Hence  the molecular effect of the mutation could be profiled at two life stages.,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,,Protocols: Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. 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 embryo rep 1,SAMEA5585429,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway",ENA FIRST PUBLIC:2021 04 30T00:25:03Z|ENA LAST UPDATE:2019 04 30T15:21:46Z|External Id:SAMEA5585429|INSDC center name:Dept. of Pharmacology and Therapeutics  College of Medicine  Nursing and Heath Sciences  National University of Ireland  Galway|INSDC first public:2021 04 30T00:25:03Z|INSDC last update:2019 04 30T15:21:46Z|INSDC status:public|Submitter Id:E MTAB 7920:Mutant embryo rep 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:Danio rerio larval stage|disease:Naxos disease|genotype:sa12692 mutant|individual:mixed pool of 10 larvae|organism part:whole organism|sample name:E MTAB 7920:Mutant embryo rep 1|scientific name:Danio rerio|strain:sa12692 mutant,,,,,,,,,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,E MTAB 7920:Mutant embryo rep 1 p,Mutant embryo rep 1 p,RNA seq of zebrafish sa12692 mutants against WT controls,Larvae were euthanized by rapid freezing. Ten larvae were pooled per sample and homogenized in TRIzol®. All centrifugation steps for RNA extractions occurred at 4°C. RNA was extracted using the TRIzol® method. Pools of 10 zebrafish larvae per biological replicate were collected at 5 dpf and placed in a 1.5 mL tube. Two adult hearts were pooled per biological replicate; these were transferred from RNAlater® to a 1.5 mL tube. TRIzol® 250 μL was added to each tube. The samples were homogenized thoroughly using a sterile 21G needle and a 1 mL syringe. Samples were incubated for 5 minutes at room temperature RT. Chloroform was added one fifth of the volume of TRIzol® used followed by immediate agitation for 15 seconds and incubation at RT for 3 minutes. For phase separation  samples were centrifuged at 12000 g for 20 min. The upper aqueous phase containing the RNA was removed carefully and transferred to a new tube. Isopropanol was added half the volume of TRIzol® used and mixed gently. Samples were incubated for 10 minutes at RT and centrifuged at 18000 g for 10 minutes. The supernatant was removed and the pellet was washed in 70% ice cold ethanol one tenth of the volume of TRIzol® used followed by centrifugation at 18000 g for 10 minutes. The ethanol was removed and the pellet was allowed to dry at RT for 7 minutes. The pellet was resuspended in 88 µL of nuclease free water and heated at 55°C for 7 minutes to fully resuspend the pellet. To remove any remaining DNA  2 µL 4 units of DNase enzyme and 10 µL of 10X DNase buffer were added and the samples were incubated for 10 minutes at 37°C. Phenol 200 µL and 20 µL of sodium acetate were added and the samples were centrifuged at 18000 g for 5 minutes. The upper phase was transferred to a new tube and 200 µL of chloroform:isoamyl alcohol 24:1 was added  followed by centrifugation at 18000 g for 5 minutes. The chloroform:isoamyl alcohol step was repeated. The upper phase was transferred to a new tube and 200 µL of isopropanol was added to precipitate the RNA. The samples 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:Danio rerio larval stage|Experimental Factor: organism part:whole organism,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,ERP115040,NextSeq 500 paired end sequencing; RNA seq of zebrafish sa12692 mutants against WT controls,ENA FIRST PUBLIC:2021 04 30|ENA LAST UPDATE:2019 04 30,HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_1.fq.gz HJGMYBGX2_Zebrafish_mRNA_17s001029_1_1_Morris_lane1Mutantembryo1_2.fq.gz,fastq fastq,6991429280.0,43696433.0,E MTAB 7920:HJGMYBGX2 Zebrafish mRNA 17s001029 1 1 Morris lane1Mutantembryo1 ,0:80 1:80,A:1852543850;C:1630880197;G:1635963943;T:1871173669;N:867621,80,80,,,1852543850,1630880197,1635963943,1871173669,867621,ERX3327065,ERS3389653,ERA1880314,"Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive","Dept. of Pharmacology and Therapeutics, College of Medicine, Nursing and Heath Sciences, National University of Ireland, Galway|European Nucleotide Archive",2,0.93819,0.95201,0.10106,0.10107,0.67541,0.67523,0.4792,0.48253,80,80,B,B,biological fallback assumption,illumina,nextseq,3prime,poly_a,trueseq,bulk,bulk,bulk,,Ireland,2019-04-30,Larval,Larval,Whole Organism,All anatomical structures
10216,ERR6501834,ERX6129007,ERS7415871,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 3,SAMEA9691614,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 3 p,Uninjured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz,fastq fastq,18723567013.0,65061888.0,E MTAB 10860:un 3 R,0:143.87 1:143.91,A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225,143,143,,,4417527025,4932613578,4960694819,4412305366,426225,ERX6129007,ERS7415871,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96755,0.96744,0.18873,0.18936,0.72868,0.73235,0.632,0.6437,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10217,ERR6501833,ERX6129006,ERS7415870,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 2,SAMEA9691613,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 2 p,Uninjured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz,fastq fastq,16871358399.0,59064661.0,E MTAB 10860:un 2 R,0:142.77 1:142.88,A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056,142,142,,,4041490134,4380856328,4414614946,4033723935,673056,ERX6129006,ERS7415870,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96589,0.9656,0.15519,0.15447,0.70887,0.71062,0.60267,0.60735,150,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10218,ERR6501832,ERX6129005,ERS7415869,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 1,SAMEA9691612,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 1 p,Uninjured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz,fastq fastq,22029484310.0,76938931.0,E MTAB 10860:un 1 R,0:143.11 1:143.22,A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752,143,143,,,5407867825,5589867496,5636111894,5394805343,831752,ERX6129005,ERS7415869,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.9602,0.95957,0.14282,0.14408,0.69649,0.69954,0.56712,0.56916,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10219,ERR6501831,ERX6129004,ERS7415868,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 3,SAMEA9691611,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 3 p,Injured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz,fastq fastq,7393087749.0,25640713.0,E MTAB 10860:in 3 R,0:144.14 1:144.20,A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175,144,144,,,1776335117,1913125420,1928181998,1775255039,190175,ERX6129004,ERS7415868,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96032,0.96001,0.15921,0.15882,0.71417,0.71869,0.59876,0.595,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10220,ERR6501830,ERX6129003,ERS7415867,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 2,SAMEA9691610,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 2 p,Injured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz,fastq fastq,9437508186.0,33059234.0,E MTAB 10860:in 2 R,0:142.70 1:142.77,A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351,142,142,,,2291798254,2421252733,2436117818,2288107030,232351,ERX6129003,ERS7415867,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96099,0.96042,0.14616,0.14802,0.70331,0.70674,0.53288,0.54459,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
10221,ERR6501829,ERX6129002,ERS7415866,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 1,SAMEA9691609,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 1 p,Injured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz,fastq fastq,15465552702.0,54194727.0,E MTAB 10860:in 1 R,0:142.59 1:142.78,A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648,142,142,,,3807777989,3911855097,3946385823,3798685145,848648,ERX6129002,ERS7415866,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.95721,0.95688,0.14331,0.14374,0.70262,0.70445,0.5114,0.52855,140,140,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System
25329,SRR25868071,SRX21589492,SRS18767065,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP4,GSM7749557,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP4,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749557,GSM7749557: sibCGFP4; Danio rerio; RNA Seq,GSM7749557 r1,GSM7749557,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP4_S46_L002_R1_001.fastq.gz WA-3548-sibCGFP4_S46_L002_R2_001.fastq.gz,fastq fastq,11996252984.0,39722692.0,GSM7749557 r1,0:151 1:151,A:3208564840;C:2791941387;G:2921724669;T:3073456372;N:565716,151,151,,,3208564840,2791941387,2921724669,3073456372,565716,SRX21589492,SRS18767065,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96224,0.96334,0.07442,0.07372,0.70595,0.70688,0.47053,0.46853,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25330,SRR25868072,SRX21589491,SRS18767064,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP3,GSM7749556,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP3,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749556,GSM7749556: sibCGFP3; Danio rerio; RNA Seq,GSM7749556 r1,GSM7749556,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP3_S45_L002_R1_001.fastq.gz WA-3548-sibCGFP3_S45_L002_R2_001.fastq.gz,fastq fastq,10113421300.0,33488150.0,GSM7749556 r1,0:151 1:151,A:2677217319;C:2366433560;G:2481164832;T:2588131881;N:473708,151,151,,,2677217319,2366433560,2481164832,2588131881,473708,SRX21589491,SRS18767064,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96295,0.96335,0.07275,0.07118,0.70654,0.7092,0.45672,0.44027,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25331,SRR25868073,SRX21589490,SRS18767063,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP2,GSM7749555,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP2,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749555,GSM7749555: sibCGFP2; Danio rerio; RNA Seq,GSM7749555 r1,GSM7749555,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP2_S44_L002_R1_001.fastq.gz WA-3548-sibCGFP2_S44_L002_R2_001.fastq.gz,fastq fastq,10142198578.0,33583439.0,GSM7749555 r1,0:151 1:151,A:2687719512;C:2375571494;G:2493046337;T:2585391111;N:470124,151,151,,,2687719512,2375571494,2493046337,2585391111,470124,SRX21589490,SRS18767063,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96241,0.96294,0.07398,0.07262,0.70524,0.70589,0.45777,0.46014,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25332,SRR25868074,SRX21589489,SRS18767062,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibCGFP1,GSM7749554,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,sibCGFP1,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ;Tg503unc:fhl2b T2A EGFP,GSM7749554,GSM7749554: sibCGFP1; Danio rerio; RNA Seq,GSM7749554 r1,GSM7749554,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibCGFP1_S43_L002_R1_001.fastq.gz WA-3548-sibCGFP1_S43_L002_R2_001.fastq.gz,fastq fastq,10994030650.0,36404075.0,GSM7749554 r1,0:151 1:151,A:2911908895;C:2573164804;G:2700790583;T:2807654156;N:512212,151,151,,,2911908895,2573164804,2700790583,2807654156,512212,SRX21589489,SRS18767062,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96119,0.96215,0.07361,0.07253,0.70632,0.7069,0.45503,0.45981,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25333,SRR25868075,SRX21589488,SRS18767059,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC4,GSM7749553,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC4,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749553,GSM7749553: sibC4; Danio rerio; RNA Seq,GSM7749553 r1,GSM7749553,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibC4_S42_L002_R1_001.fastq.gz WA-3548-sibC4_S42_L002_R2_001.fastq.gz,fastq fastq,11107320816.0,36779208.0,GSM7749553 r1,0:151 1:151,A:2945889871;C:2588267204;G:2719520712;T:2853118433;N:524596,151,151,,,2945889871,2588267204,2719520712,2853118433,524596,SRX21589488,SRS18767059,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96098,0.96213,0.07535,0.07463,0.70623,0.70749,0.42034,0.43255,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25334,SRR25868076,SRX21589487,SRS18767060,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC3,GSM7749552,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC3,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749552,GSM7749552: sibC3; Danio rerio; RNA Seq,GSM7749552 r1,GSM7749552,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibC3_S41_L002_R1_001.fastq.gz WA-3548-sibC3_S41_L002_R2_001.fastq.gz,fastq fastq,12566811014.0,41611957.0,GSM7749552 r1,0:151 1:151,A:3330340903;C:2960050871;G:3087690864;T:3188143295;N:585081,151,151,,,3330340903,2960050871,3087690864,3188143295,585081,SRX21589487,SRS18767060,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9619,0.96201,0.08592,0.08414,0.69581,0.69637,0.47091,0.47561,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25335,SRR25868077,SRX21589486,SRS18767057,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC2,GSM7749551,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC2,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749551,GSM7749551: sibC2; Danio rerio; RNA Seq,GSM7749551 r1,GSM7749551,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibC2_S40_L002_R1_001.fastq.gz WA-3548-sibC2_S40_L002_R2_001.fastq.gz,fastq fastq,9464242402.0,31338551.0,GSM7749551 r1,0:151 1:151,A:2497543137;C:2235078067;G:2319534414;T:2411649747;N:437037,151,151,,,2497543137,2235078067,2319534414,2411649747,437037,SRX21589486,SRS18767057,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96464,0.965,0.06696,0.06563,0.7138,0.71512,0.46359,0.46601,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25336,SRR25868078,SRX21589485,SRS18767061,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,sibC1,GSM7749550,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ |geo loc name:missing|collection date:missing,sibC1,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd+/ ,GSM7749550,GSM7749550: sibC1; Danio rerio; RNA Seq,GSM7749550 r1,GSM7749550,1,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,,SRP457981,,loader:fastq load.py,WA-3548-sibC1_S39_L002_R1_001.fastq.gz WA-3548-sibC1_S39_L002_R2_001.fastq.gz,fastq fastq,11153872908.0,36933354.0,GSM7749550 r1,0:151 1:151,A:2966120106;C:2600333644;G:2710289968;T:2876608337;N:520853,151,151,,,2966120106,2600333644,2710289968,2876608337,520853,SRX21589485,SRS18767061,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96189,0.96306,0.07632,0.07512,0.70749,0.70818,0.46784,0.4683,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25337,SRR25868079,SRX21589484,SRS18767058,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP4,GSM7749549,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP4,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749549,GSM7749549: dmdGFP4; Danio rerio; RNA Seq,GSM7749549 r1,GSM7749549,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP4_S54_L002_R1_001.fastq.gz WA-3548-dmdGFP4_S54_L002_R2_001.fastq.gz,fastq fastq,6593937762.0,21834231.0,GSM7749549 r1,0:151 1:151,A:1745786828;C:1531704556;G:1637507801;T:1678632967;N:305610,151,151,,,1745786828,1531704556,1637507801,1678632967,305610,SRX21589484,SRS18767058,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9626,0.96282,0.08653,0.08533,0.70433,0.70636,0.47707,0.46994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25338,SRR25868080,SRX21589483,SRS18767056,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP3,GSM7749548,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP3,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749548,GSM7749548: dmdGFP3; Danio rerio; RNA Seq,GSM7749548 r1,GSM7749548,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP3_S53_L002_R1_001.fastq.gz WA-3548-dmdGFP3_S53_L002_R2_001.fastq.gz,fastq fastq,9250573476.0,30631038.0,GSM7749548 r1,0:151 1:151,A:2485551140;C:2135752367;G:2259698711;T:2369143289;N:427969,151,151,,,2485551140,2135752367,2259698711,2369143289,427969,SRX21589483,SRS18767056,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96118,0.96196,0.0946,0.09271,0.69702,0.69834,0.47168,0.47515,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25339,SRR25868081,SRX21589482,SRS18767055,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP2,GSM7749547,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP2,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749547,GSM7749547: dmdGFP2; Danio rerio; RNA Seq,GSM7749547 r1,GSM7749547,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP2_S52_L002_R1_001.fastq.gz WA-3548-dmdGFP2_S52_L002_R2_001.fastq.gz,fastq fastq,8584886654.0,28426777.0,GSM7749547 r1,0:151 1:151,A:2310205296;C:1982936514;G:2071907465;T:2219441471;N:395908,151,151,,,2310205296,1982936514,2071907465,2219441471,395908,SRX21589482,SRS18767055,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.9586,0.95966,0.09636,0.09473,0.69881,0.6997,0.47446,0.47409,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25340,SRR25868082,SRX21589481,SRS18767052,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmdGFP1,GSM7749546,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP|geo loc name:missing|collection date:missing,dmdGFP1,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ;Tg503unc:fhl2b T2A EGFP,GSM7749546,GSM7749546: dmdGFP1; Danio rerio; RNA Seq,GSM7749546 r1,GSM7749546,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmdGFP1_S51_L002_R1_001.fastq.gz WA-3548-dmdGFP1_S51_L002_R2_001.fastq.gz,fastq fastq,7573189674.0,25076787.0,GSM7749546 r1,0:151 1:151,A:2025587174;C:1735604560;G:1848622101;T:1963022142;N:353697,151,151,,,2025587174,1735604560,1848622101,1963022142,353697,SRX21589481,SRS18767052,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.95942,0.96073,0.08752,0.08624,0.69863,0.69822,0.4733,0.47454,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25341,SRR25868083,SRX21589480,SRS18767054,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd4,GSM7749545,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd4,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749545,GSM7749545: dmd4; Danio rerio; RNA Seq,GSM7749545 r1,GSM7749545,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmd4_S50_L002_R1_001.fastq.gz WA-3548-dmd4_S50_L002_R2_001.fastq.gz,fastq fastq,9121652998.0,30204149.0,GSM7749545 r1,0:151 1:151,A:2438907102;C:2114952319;G:2225797925;T:2341561511;N:434141,151,151,,,2438907102,2114952319,2225797925,2341561511,434141,SRX21589480,SRS18767054,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.961,0.96258,0.08366,0.08276,0.69787,0.69856,0.47181,0.46112,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25342,SRR25868084,SRX21589479,SRS18767053,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd3,GSM7749544,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd3,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749544,GSM7749544: dmd3; Danio rerio; RNA Seq,GSM7749544 r1,GSM7749544,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmd3_S49_L002_R1_001.fastq.gz WA-3548-dmd3_S49_L002_R2_001.fastq.gz,fastq fastq,7896671538.0,26147919.0,GSM7749544 r1,0:151 1:151,A:2104101125;C:1828908837;G:1933039401;T:2030257090;N:365085,151,151,,,2104101125,1828908837,1933039401,2030257090,365085,SRX21589479,SRS18767053,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96014,0.96084,0.08575,0.08475,0.70082,0.70108,0.47254,0.47153,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25343,SRR25868085,SRX21589478,SRS18767051,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd2,GSM7749543,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd2,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749543,GSM7749543: dmd2; Danio rerio; RNA Seq,GSM7749543 r1,GSM7749543,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmd2_S48_L002_R1_001.fastq.gz WA-3548-dmd2_S48_L002_R2_001.fastq.gz,fastq fastq,9484006792.0,31403996.0,GSM7749543 r1,0:151 1:151,A:2518758838;C:2211640185;G:2303907076;T:2449259369;N:441324,151,151,,,2518758838,2211640185,2303907076,2449259369,441324,SRX21589478,SRS18767051,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96047,0.96128,0.09081,0.09031,0.69603,0.69605,0.46706,0.47077,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
25344,SRR25868086,SRX21589477,SRS18767050,SRP457981,PRJNA1011838,fhl2b expression ameliorates muscular dystrophy [5dpf trunk],GSE242135,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 effect of fhl2b overexpression in muscle in the background of the dmd/sapje mutant line at 5 dpf,parent bioproject:PRJNA1011837,pubmed:38431640,,dmd1,GSM7749542,,source name:5 dpf trunk|tissue:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / |geo loc name:missing|collection date:missing,dmd1,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,5 dpf trunk,,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:5 dpf trunk|cell line:dmd: t222a|cell type:zebrafish trunk|genotype:dmd / ,GSM7749542,GSM7749542: dmd1; Danio rerio; RNA Seq,GSM7749542 r1,GSM7749542,1,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,,SRP457981,,loader:fastq load.py,WA-3548-dmd1_S47_L002_R1_001.fastq.gz WA-3548-dmd1_S47_L002_R2_001.fastq.gz,fastq fastq,8411057568.0,27851184.0,GSM7749542 r1,0:151 1:151,A:2239146475;C:1963458820;G:2046268505;T:2161796444;N:387324,151,151,,,2239146475,1963458820,2046268505,2161796444,387324,SRX21589477,SRS18767050,SRA1703879,Umeå Univeristy,Umeå Univeristy,2,0.96292,0.96424,0.07952,0.07845,0.70473,0.70467,0.47569,0.47555,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,Sweden,2023-09-01,Larval,Larval,Trunk,Surface Structure
26490,SRR26034374,SRX21751583,SRS18859090,SRP459779,PRJNA1015242,Gene expression data from zebrafish SHH medulloblastoma brains and normal brains.,GSE242897,Transcriptome Analysis,Zebrafish SHH MB tumors were generated by CRISPR Cas9 mediated mutation of ptch1 in the context of tp53 heterozygous and tp53 mutant animals. Gene expression of the entire brain for ptch1 crispant animals and tp53 mutant control animals was analyzed by RNA seq. Overall design: Whole brains were collected from 3 individual tp53 mutant control animals  3 individual tp53 mutant and ptch1 crispant animals  and 3 individual tp53 heterozygous and ptch1 crispant animals.,,pubmed:39078737,,19521X3 tp53mut tumor,GSM7774459,,source name:brain|tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant|geo loc name:missing|collection date:missing,19521X3 tp53mut tumor,The Illumina adapters were trimmed using cutadapt version 1.16. Fastq files were aligned to the genome using STAR version 2.7.9a Differentially expressed genes were found using DESeq2 version 1.32.0 and the hciR package on Github. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file containing gene id  log2FC  padj  and raw counts.,brain,Brains were frozen at  80C in RNA stabilization solution QIAGEN.,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,Zebrafish were maintained in the animal facility in accordance with the Utah Institutional Animal Care and Use Committee.,tissue:brain|tumor status:tumor|age:4 wpf|genotype:tp53 mutant,GSM7774459,GSM7774459: 19521X3 tp53mut tumor; Danio rerio; RNA Seq,GSM7774459 r1,GSM7774459,1,Homogenization and total RNA isolation performed according to QIAGEN miRNeasy micro kit Qiagen 217084. Homogenization was performed with a 20 25.5 gauge needle 10 times. Samples were Dnase treated. Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold Illumina 20020598.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP459779,,loader:fastq load.py,19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R1_001.fastq.gz 19521X3_220211_A00421_0418_AHGVTMDSX3_S174_L003_R2_001.fastq.gz,fastq fastq,14792155696.0,48980648.0,GSM7774459 r1,0:151 1:151,A:4164614124;C:3233958816;G:3393302319;T:4000129008;N:151429,151,151,,,4164614124,3233958816,3393302319,4000129008,151429,SRX21751583,SRS18859090,SRA1710210,Huntsman Cancer Institute,"Oncological Sciences, University of Utah",2,0.89303,0.8944,0.32883,0.32864,0.68024,0.68091,0.48335,0.48739,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,rrna_depletion,trueseq,bulk,bulk,bulk,,United States,2023-09-11,Larval,Larval,Brain,Nervous System
26511,SRR26050756,SRX21767126,SRS18873431,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 mylz2+ cells,GSM7778667,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 4  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1 / ,GSM7778667,GSM7778667: psmb1 mutants  72hpf  biological replicate 4  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778667 r1,GSM7778667,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M4_R2_001.fastq.gz mylz2_M4_R1_001.fastq.gz,fastq fastq,16253832000.0,54179440.0,GSM7778667 r1,0:150 1:150,A:4172321085;C:3956578712;G:3980023180;T:4144541347;N:367676,150,150,,,4172321085,3956578712,3980023180,4144541347,367676,SRX21767126,SRS18873431,SRA1711572,BWH,BWH,2,0.95935,0.95662,0.03769,0.03765,0.76556,0.76741,0.42151,0.41972,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26512,SRR26050757,SRX21767125,SRS18873430,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 mylz2+ cells,GSM7778666,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 3  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1 / ,GSM7778666,GSM7778666: psmb1 mutants  72hpf  biological replicate 3  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778666 r1,GSM7778666,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M2_R1_001.fastq.gz mylz2_M2_R2_001.fastq.gz,fastq fastq,20441581200.0,68138604.0,GSM7778666 r1,0:150 1:150,A:5286416350;C:4932599128;G:4952935975;T:5269152687;N:477060,150,150,,,5286416350,4932599128,4952935975,5269152687,477060,SRX21767125,SRS18873430,SRA1711572,BWH,BWH,2,0.95599,0.95338,0.04497,0.04514,0.74811,0.74974,0.43348,0.43839,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26513,SRR26050758,SRX21767124,SRS18873429,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 mylz2+ cells,GSM7778665,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1 / |geo loc name:missing|collection date:missing,psmb1 mutants  72hpf  biological replicate 1  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1 / ,GSM7778665,GSM7778665: psmb1 mutants  72hpf  biological replicate 1  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778665 r1,GSM7778665,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_M1_R2_001.fastq.gz mylz2_M1_R1_001.fastq.gz,fastq fastq,16429988100.0,54766627.0,GSM7778665 r1,0:150 1:150,A:4233929382;C:3979539796;G:4000710274;T:4215435332;N:373316,150,150,,,4233929382,3979539796,4000710274,4215435332,373316,SRX21767124,SRS18873429,SRA1711572,BWH,BWH,2,0.95781,0.95546,0.04249,0.04266,0.75359,0.7556,0.42698,0.43387,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26514,SRR26050759,SRX21767123,SRS18873428,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 mylz2+ cells,GSM7778664,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778664,GSM7778664: psmb1 wild type/heterozygous 72hpf  biological replicate 4  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778664 r1,GSM7778664,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH4_R1_001.fastq.gz mylz2_WH4_R2_001.fastq.gz,fastq fastq,14554941600.0,48516472.0,GSM7778664 r1,0:150 1:150,A:3762464429;C:3514503319;G:3535806865;T:3741838861;N:328126,150,150,,,3762464429,3514503319,3535806865,3741838861,328126,SRX21767123,SRS18873428,SRA1711572,BWH,BWH,2,0.96121,0.95881,0.04249,0.04242,0.77745,0.77999,0.43011,0.42743,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26515,SRR26050760,SRX21767122,SRS18873427,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 mylz2+ cells,GSM7778663,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778663,GSM7778663: psmb1 wild type/heterozygous 72hpf  biological replicate 3  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778663 r1,GSM7778663,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH3_R1_001.fastq.gz mylz2_WH3_R2_001.fastq.gz,fastq fastq,14286753900.0,47622513.0,GSM7778663 r1,0:150 1:150,A:3670719741;C:3471994517;G:3491814119;T:3651899112;N:326411,150,150,,,3670719741,3471994517,3491814119,3651899112,326411,SRX21767122,SRS18873427,SRA1711572,BWH,BWH,2,0.96159,0.96038,0.03967,0.04054,0.7749,0.77644,0.43006,0.42107,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26516,SRR26050761,SRX21767121,SRS18873426,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 mylz2+ cells,GSM7778662,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778662,GSM7778662: psmb1 wild type/heterozygous 72hpf  biological replicate 2  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778662 r1,GSM7778662,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH2_R1_001.fastq.gz mylz2_WH2_R2_001.fastq.gz,fastq fastq,13505114700.0,45017049.0,GSM7778662 r1,0:150 1:150,A:3494078647;C:3258926987;G:3282303631;T:3469494662;N:310773,150,150,,,3494078647,3258926987,3282303631,3469494662,310773,SRX21767121,SRS18873426,SRA1711572,BWH,BWH,2,0.95944,0.95769,0.04602,0.04619,0.78557,0.78748,0.43504,0.43352,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular System
26517,SRR26050762,SRX21767120,SRS18873425,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 mylz2+ cells,GSM7778661,,source name:cranial mylz2+ cells muscle|tissue:cranial mylz2+ cells muscle|genotype:psmb1+/+;+/ |geo loc name:missing|collection date:missing,psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial mylz2+ 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 mylz2+ cells muscle,,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 mylz2+ cells muscle|genotype:psmb1+/+;+/ ,GSM7778661,GSM7778661: psmb1 wild type/heterozygous 72hpf  biological replicate 1  cranial mylz2+ cells; Danio rerio; RNA Seq,GSM7778661 r1,GSM7778661,1,20 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 NovaSeq 6000,,SRP460207,,loader:fastq load.py,mylz2_WH1_R1_001.fastq.gz mylz2_WH1_R2_001.fastq.gz,fastq fastq,14988184200.0,49960614.0,GSM7778661 r1,0:150 1:150,A:3819900785;C:3673988527;G:3696333011;T:3797617860;N:344017,150,150,,,3819900785,3673988527,3696333011,3797617860,344017,SRX21767120,SRS18873425,SRA1711572,BWH,BWH,2,0.96471,0.96183,0.03703,0.03679,0.77167,0.7749,0.43436,0.43348,150,150,B,B,biological fallback assumption,illumina,novaseq_era,full_length,cdna_unspecified,nextera,bulk,bulk,bulk,,United States,2023-09-13,Larval,Larval,Muscle,Muscular 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
28902,SRR26827532,SRX22524052,SRS19535497,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,vein endothelium cells  Day5 rep2,GSM7899809,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,vein endothelium cells  Day5 rep2,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899809,GSM7899809: vein endothelium cells  Day5 rep2; Danio rerio; RNA Seq,GSM7899809 r1,GSM7899809,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz,fastq fastq,9110989800.0,30369966.0,GSM7899809 r1,0:150 1:150,A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759,150,150,,,2454542720,2090617752,2126374129,2439172440,282759,SRX22524052,SRS19535497,SRA1750986,South China University of Technology,South China University of Technology,2,0.89413,0.89048,0.1507,0.14922,0.78466,0.78496,0.5263,0.5335,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28903,SRR26827533,SRX22524051,SRS19535496,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,vein endothelium cells  Day5 rep1,GSM7899808,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,vein endothelium cells  Day5 rep1,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899808,GSM7899808: vein endothelium cells  Day5 rep1; Danio rerio; RNA Seq,GSM7899808 r1,GSM7899808,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz,fastq fastq,8585973300.0,28619911.0,GSM7899808 r1,0:150 1:150,A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574,150,150,,,2253650188,2015841518,2037568162,2278266858,646574,SRX22524051,SRS19535496,SRA1750986,South China University of Technology,South China University of Technology,2,0.8876,0.88392,0.14777,0.14719,0.78969,0.79038,0.53142,0.53136,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28904,SRR26827534,SRX22524050,SRS19535495,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,non vein endothelium cells  Control  Day5 rep2,GSM7899807,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,non vein endothelium cells  Control  Day5 rep2,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899807,GSM7899807: non vein endothelium cells  Control  Day5 rep2; Danio rerio; RNA Seq,GSM7899807 r1,GSM7899807,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz,fastq fastq,9363942600.0,31213142.0,GSM7899807 r1,0:150 1:150,A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045,150,150,,,2523111369,2155598161,2171776473,2513164552,292045,SRX22524050,SRS19535495,SRA1750986,South China University of Technology,South China University of Technology,2,0.93879,0.93706,0.10971,0.10945,0.76721,0.76737,0.51346,0.51513,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28905,SRR26827535,SRX22524049,SRS19535494,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,non vein endothelium cells  Control  Day5 rep1,GSM7899806,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,non vein endothelium cells  Control  Day5 rep1,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899806,GSM7899806: non vein endothelium cells  Control  Day5 rep1; Danio rerio; RNA Seq,GSM7899806 r1,GSM7899806,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz,fastq fastq,8396176800.0,27987256.0,GSM7899806 r1,0:150 1:150,A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625,150,150,,,2190594419,1990596503,2019391921,2194713332,880625,SRX22524049,SRS19535494,SRA1750986,South China University of Technology,South China University of Technology,2,0.94508,0.94385,0.0967,0.09697,0.77642,0.77632,0.49896,0.49962,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
30032,SRR27732028,SRX23397620,SRS20258461,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 21,W 21,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-3_1.fq.gz WT72h-3_2.fq.gz,fastq fastq,6611014500.0,22036715.0,WT72h 3 1.fq.gz,0:150 1:150,A:1772431295;C:1528499931;G:1545216909;T:1764783401;N:82964,150,150,,,1772431295,1528499931,1545216909,1764783401,82964,SRX23397620,SRS20258461,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93676,0.9346,0.10556,0.10444,0.66927,0.66991,0.46155,0.46025,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30033,SRR27732029,SRX23397619,SRS20258460,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 20,W 20,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-2_1.fq.gz WT72h-2_2.fq.gz,fastq fastq,5844974100.0,19483247.0,WT72h 2 1.fq.gz,0:150 1:150,A:1570406354;C:1348972192;G:1363229634;T:1562318366;N:47554,150,150,,,1570406354,1348972192,1363229634,1562318366,47554,SRX23397619,SRS20258460,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93927,0.93723,0.10803,0.10754,0.66574,0.66959,0.45443,0.4547,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30034,SRR27732030,SRX23397618,SRS20258459,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 72 hpf embryo,zebrafish embryo 72hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:wild type|sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 19,W 19,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT72h-1_1.fq.gz WT72h-1_2.fq.gz,fastq fastq,7024123200.0,23413744.0,WT72h 1 1.fq.gz,0:150 1:150,A:1870182203;C:1638926026;G:1656247404;T:1858679271;N:88296,150,150,,,1870182203,1638926026,1656247404,1858679271,88296,SRX23397618,SRS20258459,SRA1791946,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93353,0.93369,0.09236,0.09181,0.6674,0.66789,0.44578,0.45563,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-26,Larval,Larval,Embryo Imprecise,All anatomical structures
30049,SRR27730712,SRX23396346,SRS20257260,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 42,W 42,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-3_1.fq.gz hamp72h-3_2.fq.gz,fastq fastq,7124946000.0,23749820.0,hamp72h 3 1.fq.gz,0:150 1:150,A:1926386901;C:1633268260;G:1649597432;T:1915633812;N:59595,150,150,,,1926386901,1633268260,1649597432,1915633812,59595,SRX23396346,SRS20257260,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9369,0.9352,0.10335,0.10255,0.66703,0.6686,0.47407,0.46796,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30051,SRR27730714,SRX23396344,SRS20257258,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 41,W 41,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-2_1.fq.gz hamp72h-2_2.fq.gz,fastq fastq,6201979200.0,20673264.0,hamp72h 2 1.fq.gz,0:150 1:150,A:1657650097;C:1440501731;G:1451375517;T:1652374388;N:77467,150,150,,,1657650097,1440501731,1451375517,1652374388,77467,SRX23396344,SRS20257258,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93468,0.9333,0.0972,0.09614,0.66427,0.66588,0.46658,0.46539,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30052,SRR27730715,SRX23396343,SRS20257257,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /  72 hpf embryo,zebrafish embryo hamp /  72hpf replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|dev stage:72 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:hamp / |sample type:whole organism|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio rerio: 72hpf embryo,W 40,W 40,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,hamp72h-1_1.fq.gz hamp72h-1_2.fq.gz,fastq fastq,6432009000.0,21440030.0,hamp72h 1 1.fq.gz,0:150 1:150,A:1734564732;C:1478070668;G:1490938268;T:1728354590;N:80742,150,150,,,1734564732,1478070668,1490938268,1728354590,80742,SRX23396343,SRS20257257,SRA1791861,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.93382,0.93132,0.10621,0.10453,0.66592,0.66667,0.46409,0.46541,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-01-25,Larval,Larval,Embryo Imprecise,All anatomical structures
30560,SRR27836075,SRX23499416,SRS20351174,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 4  21 dpf,GSM8059034,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 4  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059034,GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq,GSM8059034 r1,GSM8059034,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_4_S8_L001_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L001_R2_001.fastq.gz,fastq fastq,2533252722.0,24835811.0,GSM8059034 r1,0:51 1:51,A:767895104;C:496128064;G:502250517;T:766951391;N:27646,51,51,,,767895104,496128064,502250517,766951391,27646,SRX23499416,SRS20351174,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30561,SRR27836076,SRX23499416,SRS20351174,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 4  21 dpf,GSM8059034,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 4  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059034,GSM8059034: rbpms2 mutant 4  21 dpf; Danio rerio; RNA Seq,GSM8059034 r1,GSM8059034,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_4_S8_L002_R1_001.fastq.gz rbpms2-d21-DM_4_S8_L002_R2_001.fastq.gz,fastq fastq,2500214514.0,24511907.0,GSM8059034 r2,0:51 1:51,A:757980090;C:489633622;G:495839519;T:756737989;N:23294,51,51,,,757980090,489633622,495839519,756737989,23294,SRX23499416,SRS20351174,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30562,SRR27836077,SRX23499415,SRS20351173,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 3  21 dpf,GSM8059033,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 3  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059033,GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq,GSM8059033 r1,GSM8059033,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_3_S7_L001_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L001_R2_001.fastq.gz,fastq fastq,2383569354.0,23368327.0,GSM8059033 r1,0:51 1:51,A:705650487;C:468856307;G:473479720;T:735556568;N:26272,51,51,,,705650487,468856307,473479720,735556568,26272,SRX23499415,SRS20351173,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30563,SRR27836078,SRX23499415,SRS20351173,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 3  21 dpf,GSM8059033,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 3  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059033,GSM8059033: rbpms2 mutant 3  21 dpf; Danio rerio; RNA Seq,GSM8059033 r1,GSM8059033,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_3_S7_L002_R1_001.fastq.gz rbpms2-d21-DM_3_S7_L002_R2_001.fastq.gz,fastq fastq,2324856114.0,22792707.0,GSM8059033 r2,0:51 1:51,A:688232198;C:457346277;G:462034541;T:717221485;N:21613,51,51,,,688232198,457346277,462034541,717221485,21613,SRX23499415,SRS20351173,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30564,SRR27836079,SRX23499414,SRS20351172,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 1  21 dpf,GSM8059032,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 1  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059032,GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq,GSM8059032 r1,GSM8059032,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_1_S5_L001_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L001_R2_001.fastq.gz,fastq fastq,2412458100.0,23651550.0,GSM8059032 r1,0:51 1:51,A:726246267;C:465733066;G:465377798;T:755071663;N:29306,51,51,,,726246267,465733066,465377798,755071663,29306,SRX23499414,SRS20351172,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30565,SRR27836080,SRX23499414,SRS20351172,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 mutant 1  21 dpf,GSM8059032,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM|geo loc name:missing|collection date:missing,rbpms2 mutant 1  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:rbpms2a ae30; rbpms2b sa MM,GSM8059032,GSM8059032: rbpms2 mutant 1  21 dpf; Danio rerio; RNA Seq,GSM8059032 r1,GSM8059032,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-DM_1_S5_L002_R1_001.fastq.gz rbpms2-d21-DM_1_S5_L002_R2_001.fastq.gz,fastq fastq,2363898144.0,23175472.0,GSM8059032 r2,0:51 1:51,A:711756208;C:456236364;G:456088591;T:739792903;N:24078,51,51,,,711756208,456236364,456088591,739792903,24078,SRX23499414,SRS20351172,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30566,SRR27836081,SRX23499413,SRS20351171,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 3  21 dpf,GSM8059031,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 3  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059031,GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq,GSM8059031 r1,GSM8059031,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_3_S3_L001_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L001_R2_001.fastq.gz,fastq fastq,2048418162.0,20082531.0,GSM8059031 r1,0:51 1:51,A:612611264;C:409068349;G:413909657;T:612805097;N:23795,51,51,,,612611264,409068349,413909657,612805097,23795,SRX23499413,SRS20351171,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30567,SRR27836082,SRX23499413,SRS20351171,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 3  21 dpf,GSM8059031,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 3  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059031,GSM8059031: rbpms2 wildtype 3  21 dpf; Danio rerio; RNA Seq,GSM8059031 r1,GSM8059031,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_3_S3_L002_R1_001.fastq.gz rbpms2-d21-WT_3_S3_L002_R2_001.fastq.gz,fastq fastq,2018915070.0,19793285.0,GSM8059031 r2,0:51 1:51,A:603776465;C:403221066;G:408169193;T:603728354;N:19992,51,51,,,603776465,403221066,408169193,603728354,19992,SRX23499413,SRS20351171,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30568,SRR27836083,SRX23499412,SRS20351179,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 2  21 dpf,GSM8059030,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 2  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059030,GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq,GSM8059030 r1,GSM8059030,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_2_S2_L001_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L001_R2_001.fastq.gz,fastq fastq,1927777866.0,18899783.0,GSM8059030 r1,0:51 1:51,A:589122616;C:372230241;G:374787285;T:591617780;N:19944,51,51,,,589122616,372230241,374787285,591617780,19944,SRX23499412,SRS20351179,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30569,SRR27836084,SRX23499412,SRS20351179,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 2  21 dpf,GSM8059030,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 2  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059030,GSM8059030: rbpms2 wildtype 2  21 dpf; Danio rerio; RNA Seq,GSM8059030 r1,GSM8059030,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_2_S2_L002_R1_001.fastq.gz rbpms2-d21-WT_2_S2_L002_R2_001.fastq.gz,fastq fastq,1901436570.0,18641535.0,GSM8059030 r2,0:51 1:51,A:581077435;C:367152917;G:369822980;T:583366137;N:17101,51,51,,,581077435,367152917,369822980,583366137,17101,SRX23499412,SRS20351179,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30570,SRR27836085,SRX23499411,SRS20351170,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 1  21 dpf,GSM8059029,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 1  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059029,GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq,GSM8059029 r1,GSM8059029,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_1_S1_L001_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L001_R2_001.fastq.gz,fastq fastq,1878693222.0,18418561.0,GSM8059029 r1,0:51 1:51,A:581058368;C:356028122;G:360378733;T:581204723;N:23276,51,51,,,581058368,356028122,360378733,581204723,23276,SRX23499411,SRS20351170,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
30571,SRR27836086,SRX23499411,SRS20351170,SRP487485,PRJNA1072072,Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component  Mios,GSE254850,Transcriptome Analysis,Reproductive success relies on proper establishment and maintenance of biological sex. In many animals  including mammals  the primary gonad is initially ovary in character. We previously showed the RNA binding protein RNAbp  Rbpms2  is required for ovary fate in zebrafish. Here  we identified Rbpms2 targets in oocytesRbpms2 bound oocyte RNAs; rboRNAs. We identify Rbpms2 as a translational regulator ofrboRNAs  which include testis factors and ribosome biogenesis factors. Further  genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway  specifically through the mTorc1 activating Gap activity towards Rags 2 Gator2 component  Missing oocyte Mios. Cumulatively  our findings indicate that early gonocytes are in a dual poised  bipotential state in which Rbpms2 acts as a binary fate switch. Specifically  Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2 mediated checkpoint  thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis. Overall design: To determine the RNA targets of Rbpms2  we generated wildtype female zebrafish expressing Rbpms2 mApple or mApple alone fusion proteins exclusively in the germline. Immunoprecipitation was performed in 2 adult female ovaries per transgene. Crosslinked and uncrosslinked samples for Rbpms2 mApple expressing fish and crosslined and uncrosslinked samples for mApple expressing fish were sequenced. RNAs found in the Rbpms2 mApple crosslinked and the mApple crosslinked and uncrosslinked datasets that were also present in the Rbpms2 mApple uncrosslinked dataset were excluded. RNAs present only in the uncrosslinked datasets were counted as RNA targets of Rbpms2. To characterize the transcriptional differences of rbpms2 mutants vs wildtype fish prior to sex determination 21 dpf  we performed bulk RNA sequencing on n=3 dpf 21 dpf wildtype and n=3 rbpms2 mutant fish. DESeq was then performed for Differential Gene Expression Analysis.,,pubmed:38898112,,rbpms2 wildtype 1  21 dpf,GSM8059029,,source name:Gonad|tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype|geo loc name:missing|collection date:missing,rbpms2 wildtype 1  21 dpf,Expression count STAR basepair pipeline was used GRCz10 XLSX file includes all gene ids  symbols  counts  FPKMs  and TPMs for each sample CSV files include gene id  symbol  count  FPKM  and TPM for each sample,Gonad,,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,tissue:Gonad|cell type:Germline and somatic|genotype:Wildtype,GSM8059029,GSM8059029: rbpms2 wildtype 1  21 dpf; Danio rerio; RNA Seq,GSM8059029 r1,GSM8059029,1,RNA was extracted from individual tissues using an Agilent Absolutely RNA Nanoprep Kit 400753 Libraries were generated with a low input SMART Seq HT with Nxt HT kit Clontech Laboratories  634947,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP487485,,loader:fastq load.py,rbpms2-d21-WT_1_S1_L002_R1_001.fastq.gz rbpms2-d21-WT_1_S1_L002_R2_001.fastq.gz,fastq fastq,1861916160.0,18254080.0,GSM8059029 r2,0:51 1:51,A:575859972;C:352771580;G:357641601;T:575624138;N:18869,51,51,,,575859972,352771580,357641601,575624138,18869,SRX23499411,SRS20351170,SRA1796363,"Marlow, CDRB, Icahn School of Medicine Mount Sinai","Marlow, CDRB, Icahn School of Medicine Mount Sinai",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-02-01,Larval,Larval,Gonad,Reproductive System
32488,SRR29285561,SRX24802703,SRS21518811,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 8dpf 5,GSM8305920,,source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:5|geo loc name:missing|collection date:missing,Mutant 8dpf 5,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:5,GSM8305920,GSM8305920: Mutant 8dpf 5; Danio rerio; RNA Seq,GSM8305920 r1,GSM8305920,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,30_S30_R1_001.fastq.gz 30_S30_R2_001.fastq.gz,fastq fastq,6296757573.0,23640034.0,GSM8305920 r1,0:133.22 1:133.14,A:1705780530;C:1407325553;G:1444855023;T:1711961543;N:26834924,133,133,,,1705780530,1407325553,1444855023,1711961543,26834924,SRX24802703,SRS21518811,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.72886,0.72666,0.24329,0.24823,0.73529,0.74146,0.51326,0.51598,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32489,SRR29285562,SRX24802702,SRS21518810,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 8dpf 4,GSM8305919,,source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:4|geo loc name:missing|collection date:missing,Mutant 8dpf 4,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:4,GSM8305919,GSM8305919: Mutant 8dpf 4; Danio rerio; RNA Seq,GSM8305919 r1,GSM8305919,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,29_S29_R1_001.fastq.gz 29_S29_R2_001.fastq.gz,fastq fastq,3977478302.0,15484604.0,GSM8305919 r1,0:128.40 1:128.47,A:1153124522;C:795067209;G:830421153;T:1174546124;N:24319294,128,128,,,1153124522,795067209,830421153,1174546124,24319294,SRX24802702,SRS21518810,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.75548,0.75663,0.31871,0.33308,0.72275,0.73411,0.59066,0.60265,148,148,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32490,SRR29285563,SRX24802701,SRS21518809,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 8dpf 3,GSM8305918,,source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:3|geo loc name:missing|collection date:missing,Mutant 8dpf 3,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:3,GSM8305918,GSM8305918: Mutant 8dpf 3; Danio rerio; RNA Seq,GSM8305918 r1,GSM8305918,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,28_S28_R1_001.fastq.gz 28_S28_R2_001.fastq.gz,fastq fastq,1621059592.0,6158743.0,GSM8305918 r1,0:131.56 1:131.65,A:440443017;C:360750685;G:369447031;T:443711271;N:6707588,131,131,,,440443017,360750685,369447031,443711271,6707588,SRX24802701,SRS21518809,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.80702,0.80741,0.30093,0.30284,0.72563,0.73269,0.58822,0.62115,121,121,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32491,SRR29285564,SRX24802700,SRS21518808,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 8dpf 2,GSM8305917,,source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:2|geo loc name:missing|collection date:missing,Mutant 8dpf 2,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:2,GSM8305917,GSM8305917: Mutant 8dpf 2; Danio rerio; RNA Seq,GSM8305917 r1,GSM8305917,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,27_S27_R1_001.fastq.gz 27_S27_R2_001.fastq.gz,fastq fastq,14150299985.0,54393342.0,GSM8305917 r1,0:130.00 1:130.15,A:4019553056;C:2916143925;G:3025489536;T:4096585966;N:92527502,130,130,,,4019553056,2916143925,3025489536,4096585966,92527502,SRX24802700,SRS21518808,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.7951,0.79615,0.295,0.30615,0.72516,0.73367,0.59737,0.60496,70,70,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32492,SRR29285565,SRX24802699,SRS21518807,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 8dpf 1,GSM8305916,,source name:whole body|tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:1|geo loc name:missing|collection date:missing,Mutant 8dpf 1,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:8dpf|genotype:Mutant|replicate:1,GSM8305916,GSM8305916: Mutant 8dpf 1; Danio rerio; RNA Seq,GSM8305916 r1,GSM8305916,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,26_S26_R1_001.fastq.gz 26_S26_R2_001.fastq.gz,fastq fastq,1761064863.0,6874590.0,GSM8305916 r1,0:127.98 1:128.19,A:497556179;C:351357168;G:364495411;T:507457398;N:40198707,127,128,,,497556179,351357168,364495411,507457398,40198707,SRX24802699,SRS21518807,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.61484,0.60165,0.21597,0.22261,0.7614,0.77402,0.57726,0.59475,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32493,SRR29285566,SRX24802698,SRS21518806,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 5dpf 5,GSM8305915,,source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:5|geo loc name:missing|collection date:missing,Mutant 5dpf 5,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:5,GSM8305915,GSM8305915: Mutant 5dpf 5; Danio rerio; RNA Seq,GSM8305915 r1,GSM8305915,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,20_S20_R1_001.fastq.gz 20_S20_R2_001.fastq.gz,fastq fastq,44861994269.0,170464414.0,GSM8305915 r1,0:131.53 1:131.64,A:12814834357;C:9164689606;G:9481668356;T:13176021007;N:224780943,131,131,,,12814834357,9164689606,9481668356,13176021007,224780943,SRX24802698,SRS21518806,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.76449,0.75903,0.29761,0.31015,0.72088,0.73399,0.58295,0.58975,78,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32494,SRR29285567,SRX24802697,SRS21518805,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 5dpf 4,GSM8305914,,source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:4|geo loc name:missing|collection date:missing,Mutant 5dpf 4,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:4,GSM8305914,GSM8305914: Mutant 5dpf 4; Danio rerio; RNA Seq,GSM8305914 r1,GSM8305914,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,19_S19_R1_001.fastq.gz 19_S19_R2_001.fastq.gz,fastq fastq,5607120194.0,22270005.0,GSM8305914 r1,0:125.80 1:125.98,A:1567782157;C:1175882461;G:1212477800;T:1586827542;N:64150234,125,125,,,1567782157,1175882461,1212477800,1586827542,64150234,SRX24802697,SRS21518805,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.73788,0.74164,0.26347,0.27285,0.73914,0.74688,0.59711,0.60862,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32495,SRR29285568,SRX24802696,SRS21518804,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 5dpf 3,GSM8305913,,source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:3|geo loc name:missing|collection date:missing,Mutant 5dpf 3,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:3,GSM8305913,GSM8305913: Mutant 5dpf 3; Danio rerio; RNA Seq,GSM8305913 r1,GSM8305913,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,18_S18_R1_001.fastq.gz 18_S18_R2_001.fastq.gz,fastq fastq,35413242014.0,147228358.0,GSM8305913 r1,,,,,,,,,,,,SRX24802696,SRS21518804,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.62906,0.62092,0.3537,0.37017,0.75465,0.76822,0.54776,0.569,137,137,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32496,SRR29285569,SRX24802695,SRS21518803,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 5dpf 2,GSM8305912,,source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:2|geo loc name:missing|collection date:missing,Mutant 5dpf 2,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:2,GSM8305912,GSM8305912: Mutant 5dpf 2; Danio rerio; RNA Seq,GSM8305912 r1,GSM8305912,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,17_S17_R1_001.fastq.gz 17_S17_R2_001.fastq.gz,fastq fastq,35865106141.0,138431350.0,GSM8305912 r1,0:129.49 1:129.59,A:10011943989;C:7650430976;G:7850227100;T:10118820207;N:233683869,129,129,,,10011943989,7650430976,7850227100,10118820207,233683869,SRX24802695,SRS21518803,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.59494,0.59416,0.20522,0.21104,0.77297,0.781,0.63558,0.6401,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32497,SRR29285570,SRX24802694,SRS21518802,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,Mutant 5dpf 1,GSM8305911,,source name:whole body|tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:1|geo loc name:missing|collection date:missing,Mutant 5dpf 1,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:Mutant|age:5dpf|genotype:WT|replicate:1,GSM8305911,GSM8305911: Mutant 5dpf 1; Danio rerio; RNA Seq,GSM8305911 r1,GSM8305911,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,16_S16_R1_001.fastq.gz 16_S16_R2_001.fastq.gz,fastq fastq,11424421439.0,43844065.0,GSM8305911 r1,0:130.34 1:130.23,A:3153455776;C:2478215013;G:2568391366;T:3186999856;N:37359428,130,130,,,3153455776,2478215013,2568391366,3186999856,37359428,SRX24802694,SRS21518802,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.80218,0.80263,0.28757,0.2949,0.73442,0.74474,0.61946,0.63013,150,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32498,SRR29285571,SRX24802693,SRS21518801,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 8dpf 5,GSM8305910,,source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:5|geo loc name:missing|collection date:missing,WT 8dpf 5,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:5,GSM8305910,GSM8305910: WT 8dpf 5; Danio rerio; RNA Seq,GSM8305910 r1,GSM8305910,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,15_S15_R1_001.fastq.gz 15_S15_R2_001.fastq.gz,fastq fastq,7264574863.0,26944269.0,GSM8305910 r1,0:134.76 1:134.85,A:2143925256;C:1439783329;G:1477108393;T:2165189668;N:38568217,134,134,,,2143925256,1439783329,1477108393,2165189668,38568217,SRX24802693,SRS21518801,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.37678,0.37076,0.18096,0.18839,0.80211,0.81373,0.56741,0.58443,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32499,SRR29285572,SRX24802692,SRS21518800,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 8dpf 4,GSM8305909,,source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:4|geo loc name:missing|collection date:missing,WT 8dpf 4,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:4,GSM8305909,GSM8305909: WT 8dpf 4; Danio rerio; RNA Seq,GSM8305909 r1,GSM8305909,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,14_S14_R1_001.fastq.gz 14_S14_R2_001.fastq.gz,fastq fastq,32778065815.0,131056842.0,GSM8305909 r1,,,,,,,,,,,,SRX24802692,SRS21518800,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.78701,0.78678,0.27772,0.2804,0.74507,0.75122,0.62456,0.6297,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32500,SRR29285573,SRX24802691,SRS21518799,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 8dpf 3,GSM8305908,,source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:3|geo loc name:missing|collection date:missing,WT 8dpf 3,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:3,GSM8305908,GSM8305908: WT 8dpf 3; Danio rerio; RNA Seq,GSM8305908 r1,GSM8305908,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,13_S13_R1_001.fastq.gz 13_S13_R2_001.fastq.gz,fastq fastq,2715775308.0,12018782.0,GSM8305908 r1,0:112.87 1:113.09,A:793819995;C:525097564;G:555570458;T:797117723;N:44169568,112,113,,,793819995,525097564,555570458,797117723,44169568,SRX24802691,SRS21518799,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.6927,0.68987,0.40365,0.41469,0.74276,0.75175,0.57052,0.56713,108,108,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32501,SRR29285574,SRX24802690,SRS21518798,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 8dpf 2,GSM8305907,,source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:2|geo loc name:missing|collection date:missing,WT 8dpf 2,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:2,GSM8305907,GSM8305907: WT 8dpf 2; Danio rerio; RNA Seq,GSM8305907 r1,GSM8305907,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,12_S12_R1_001.fastq.gz 12_S12_R2_001.fastq.gz,fastq fastq,13984059501.0,53799424.0,GSM8305907 r1,0:129.96 1:129.97,A:3756098800;C:3181863043;G:3231146344;T:3789534545;N:25416769,129,129,,,3756098800,3181863043,3231146344,3789534545,25416769,SRX24802690,SRS21518798,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.86656,0.86486,0.30024,0.30172,0.72537,0.72914,0.61466,0.62287,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32502,SRR29285575,SRX24802689,SRS21518797,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 8dpf 1,GSM8305906,,source name:whole body|tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:1|geo loc name:missing|collection date:missing,WT 8dpf 1,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:8dpf|genotype:Mutant|replicate:1,GSM8305906,GSM8305906: WT 8dpf 1; Danio rerio; RNA Seq,GSM8305906 r1,GSM8305906,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,11_S11_R1_001.fastq.gz 11_S11_R2_001.fastq.gz,fastq fastq,5388226113.0,22114932.0,GSM8305906 r1,0:121.71 1:121.94,A:1571088373;C:1056285467;G:1094594072;T:1584231174;N:82027027,121,121,,,1571088373,1056285467,1094594072,1584231174,82027027,SRX24802689,SRS21518797,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.60126,0.60282,0.28098,0.29016,0.76337,0.7713,0.59511,0.60885,90,90,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32503,SRR29285576,SRX24802688,SRS21518796,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 5dpf 5,GSM8305905,,source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:5|geo loc name:missing|collection date:missing,WT 5dpf 5,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:5,GSM8305905,GSM8305905: WT 5dpf 5; Danio rerio; RNA Seq,GSM8305905 r1,GSM8305905,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,5_S5_R1_001.fastq.gz 5_S5_R2_001.fastq.gz,fastq fastq,36864973430.0,147827522.0,GSM8305905 r1,0:124.60 1:124.78,A:10882747927;C:7449801226;G:7566579083;T:10815945515;N:149899679,124,124,,,10882747927,7449801226,7566579083,10815945515,149899679,SRX24802688,SRS21518796,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.47374,0.48165,0.40857,0.41507,0.81677,0.81471,0.49158,0.49375,150,91,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32504,SRR29285577,SRX24802687,SRS21518795,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 5dpf 4,GSM8305904,,source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:4|geo loc name:missing|collection date:missing,WT 5dpf 4,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:4,GSM8305904,GSM8305904: WT 5dpf 4; Danio rerio; RNA Seq,GSM8305904 r1,GSM8305904,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,4_S4_R1_001.fastq.gz 4_S4_R2_001.fastq.gz,fastq fastq,20865362996.0,85474604.0,GSM8305904 r1,0:121.96 1:122.16,A:6011091272;C:4396318913;G:4448338805;T:5974192691;N:35421315,121,122,,,6011091272,4396318913,4448338805,5974192691,35421315,SRX24802687,SRS21518795,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.687,0.69172,0.58591,0.59047,0.76589,0.76607,0.51259,0.52162,84,84,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32505,SRR29285578,SRX24802686,SRS21518794,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 5dpf 3,GSM8305903,,source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:3|geo loc name:missing|collection date:missing,WT 5dpf 3,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:3,GSM8305903,GSM8305903: WT 5dpf 3; Danio rerio; RNA Seq,GSM8305903 r1,GSM8305903,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,3_S3_R1_001.fastq.gz 3_S3_R2_001.fastq.gz,fastq fastq,44771347433.0,163809987.0,GSM8305903 r1,0:136.62 1:136.70,A:13512158868;C:8775800809;G:8933321442;T:13479562694;N:70503620,136,136,,,13512158868,8775800809,8933321442,13479562694,70503620,SRX24802686,SRS21518794,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.74877,0.75623,0.64593,0.65183,0.73434,0.73537,0.49765,0.49588,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32506,SRR29285579,SRX24802685,SRS21518793,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 5dpf 2,GSM8305902,,source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:2|geo loc name:missing|collection date:missing,WT 5dpf 2,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:2,GSM8305902,GSM8305902: WT 5dpf 2; Danio rerio; RNA Seq,GSM8305902 r1,GSM8305902,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,2_S2_R1_001.fastq.gz 2_S2_R2_001.fastq.gz,fastq fastq,52117152588.0,201316650.0,GSM8305902 r1,0:129.38 1:129.51,A:14844703814;C:10642718902;G:11093806467;T:15180220229;N:355703176,129,129,,,14844703814,10642718902,11093806467,15180220229,355703176,SRX24802685,SRS21518793,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.77169,0.7713,0.2982,0.30914,0.72557,0.73752,0.59505,0.60502,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
32507,SRR29285580,SRX24802684,SRS21518792,SRP511787,PRJNA1120060,O GlcNAcylation Modulates Expression and Abundance of N Glycosylation Machinery in an Inherited Glycosylation Disorder,GSE269074,Transcriptome Analysis,Much of the N glycosylation machinery was identified decades ago  but the regulatory mechanisms influencing normal and disease states are only beginning to be discovered. Recent studies highlight a role for key metabolites and metabolic enzymes in this process  revising the view of the relationship between different metabolic pathways. Using a multi omic approach in a zebrafish  we discovered a mechanism where O GlcNAcylation directly influences the expression and abundance of two enzymes essential for the earliest steps of N linked glycosylation  the nus1 encoded NgBR and Dpagt1. Here we show that phosphomannomutase pmm2 deficiency is associated with increased levels of UDP GlcNAc and protein O GlcNAcylation. Biochemical studies show that O GlcNAc modification of the NgBR and Dpagt1 increases their abundance in pmm2m/m mutants. Modulating O GlcNAc levels  NgBR abundance or Dpagt1 activity exacerbated cartilage phenotypes in pmm2 mutants  suggesting that O GlcNAc mediated increases in the N glycosylation machinery protects against more severe pathology.  These findings highlight nucleotide sugar donors as metabolic sensors that coordinate two different glycosylation pathways  demonstrating how their interplay is relevant to disease outcome in the most common congenital disorder of glycosylation. Overall design: We did bulk total RNA seq with ribo depletion of whole zebrafish larvae at 2 ages  5dpf and 8dpf for two genotypes  wildtype WT and Mutant where the mutant is a loss of function of Pmm2. Each sample consisted of 15 larvae and we  sequenced 5 biological replicates per genotype and age combination.,,pubmed:39561044,,WT 5dpf 1,GSM8305901,,source name:whole body|tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:1|geo loc name:missing|collection date:missing,WT 5dpf 1,FASTQ QC by fastp adapter trimming and assessment of ribo depletion by bbduk alignment by STAR BAM indexing by samtools counting of reads in each gene by subread Assembly: GRCz11 Supplementary files format and content: The counts table contains raw counts of reads aligning to genes generated by subread. It is a tab delimited text file,whole body,For the sample preparation  3dpf larvae were genotyped using the assay described see the qRT PCR analyses and genotyping section  subsequently pooled by genotype and collected and snap frozen in liquid nitrogen 5 and 8dpf. 15 larvae per genotype per sample were collected.,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,Animals were maintained according to standard protocols,tissue:whole body|genotype:WT|age:5dpf|genotype:WT|replicate:1,GSM8305901,GSM8305901: WT 5dpf 1; Danio rerio; RNA Seq,GSM8305901 r1,GSM8305901,1,Direct zol RNA microprep kit KTC UNIV RNA Seq NUQ AD A01 with NuQuant Custom deplete ADU033 D. rerio kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP511787,,,1_S1_R2_001.fastq.gz 1_S1_R1_001.fastq.gz,fastq fastq,41102336514.0,146454940.0,GSM8305901 r1,0:140.30 1:140.35,A:12296287974;C:8083080687;G:8218018380;T:12249171413;N:255778060,140,140,,,12296287974,8083080687,8218018380,12249171413,255778060,SRX24802684,SRS21518792,SRA1889334,Greenwood Genetic Center,Greenwood Genetic Center,2,0.07796,0.07849,0.03932,0.04037,0.93685,0.94028,0.58171,0.59475,149,149,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2024-06-04,Larval,Larval,Trunk,Surface Structure
33934,SRR30947094,SRX26349630,SRS22874784,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #3,GSM8565205,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #3,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565205,GSM8565205: whole heart  tak1+/+ wild type  replicate #3; Danio rerio; RNA Seq,GSM8565205 r1,GSM8565205,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_3_1.fq.gz WT_3_2.fq.gz,fastq fastq,4449566200.0,22247831.0,GSM8565205 r1,0:100 1:100,A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0,100,100,,,1179341017,1046638560,1046356098,1177230525,0,SRX26349630,SRS22874784,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33935,SRR30947095,SRX26349629,SRS22874783,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #2,GSM8565204,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #2,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565204,GSM8565204: whole heart  tak1+/+ wild type  replicate #2; Danio rerio; RNA Seq,GSM8565204 r1,GSM8565204,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_2_1.fq.gz WT_2_2.fq.gz,fastq fastq,4519627600.0,22598138.0,GSM8565204 r1,0:100 1:100,A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0,100,100,,,1207344552,1055139553,1056806709,1200336786,0,SRX26349629,SRS22874783,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33936,SRR30947096,SRX26349628,SRS22874781,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1+/+ wild type  replicate #1,GSM8565203,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing,whole heart  tak1+/+ wild type  replicate #1,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1+/+,GSM8565203,GSM8565203: whole heart  tak1+/+ wild type  replicate #1; Danio rerio; RNA Seq,GSM8565203 r1,GSM8565203,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,WT_1_1.fq.gz WT_1_2.fq.gz,fastq fastq,4496601200.0,22483006.0,GSM8565203 r1,0:100 1:100,A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0,100,100,,,1201390946,1050348674,1051355386,1193506194,0,SRX26349628,SRS22874781,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33937,SRR30947097,SRX26349627,SRS22874780,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #3,GSM8565202,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #3,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565202,GSM8565202: whole heart  tak1 /  mutant  replicate #3; Danio rerio; RNA Seq,GSM8565202 r1,GSM8565202,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_3_1.fq.gz mut_3_2.fq.gz,fastq fastq,4451759600.0,22258798.0,GSM8565202 r1,0:100 1:100,A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0,100,100,,,1167798041,1064608876,1066460994,1152891689,0,SRX26349627,SRS22874780,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33938,SRR30947098,SRX26349626,SRS22874782,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #2,GSM8565201,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #2,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565201,GSM8565201: whole heart  tak1 /  mutant  replicate #2; Danio rerio; RNA Seq,GSM8565201 r1,GSM8565201,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_2_1.fq.gz mut_2_2.fq.gz,fastq fastq,4534495200.0,22672476.0,GSM8565201 r1,,,,,,,,,,,,SRX26349626,SRS22874782,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
33939,SRR30947099,SRX26349625,SRS22874779,SRP537826,PRJNA1171482,TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development,GSE279246,Transcriptome Analysis,Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.,,,,whole heart  tak1 /  mutant  replicate #1,GSM8565200,,source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing,whole heart  tak1 /  mutant  replicate #1,post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.,Whole heart  3 dpf,,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,tissue:Whole heart  3 dpf|genotype:tak1 / ,GSM8565200,GSM8565200: whole heart  tak1 /  mutant  replicate #1; Danio rerio; RNA Seq,GSM8565200 r1,GSM8565200,1,RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP537826,,,mut_1_1.fq.gz mut_1_2.fq.gz,fastq fastq,4425052600.0,22125263.0,GSM8565200 r1,0:100 1:100,A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0,100,100,,,1161989932,1055452567,1055912540,1151697561,0,SRX26349625,SRS22874779,SRA1990217,"Department of Cellular and Molecular Medicine, University of Copenhagen","Department of Cellular and Molecular Medicine, University of Copenhagen",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,Denmark,2024-10-10,Larval,Larval,Heart,Cardiovascular System
34192,SRR31443228,SRX26812023,SRS23296672,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 3,srrm4[y712] mutant replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut3.pass2Aligned.sortedByCoord.out.bam,bam,23466336192.0,117587529.0,25938 mut3.pass2Aligned.sortedByCoord.out.bam,0:100.13 1:100.08,A:6298034402;C:5433884683;G:5344985734;T:6388443446;N:987927,100,100,,,6298034402,5433884683,5344985734,6388443446,987927,SRX26812023,SRS23296672,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95864,0.95894,0.10681,0.1052,0.65385,0.65403,0.46511,0.46252,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34193,SRR31443229,SRX26812022,SRS23296671,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 3,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 3,srrm4[y712] wild type replicate 3,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt3.pass2Aligned.sortedByCoord.out.bam,bam,23979171134.0,120156039.0,25938 wt3.pass2Aligned.sortedByCoord.out.bam,0:100.12 1:100.07,A:6398807397;C:5589997524;G:5503127729;T:6486232627;N:1005857,100,100,,,6398807397,5589997524,5503127729,6486232627,1005857,SRX26812022,SRS23296671,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.95941,0.96004,0.10323,0.10191,0.65451,0.6532,0.46396,0.46398,101,100,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34194,SRR31443230,SRX26812021,SRS23296670,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 2,srrm4[y712] mutant replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut2.pass2Aligned.sortedByCoord.out.bam,bam,20256127500.0,101792067.0,25938 mut2.pass2Aligned.sortedByCoord.out.bam,0:100.05 1:100.00,A:5435798119;C:4683997479;G:4650293108;T:5485187428;N:851366,100,100,,,5435798119,4683997479,4650293108,5485187428,851366,SRX26812021,SRS23296670,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96008,0.96049,0.10232,0.10156,0.66072,0.65932,0.4668,0.46817,95,95,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34195,SRR31443231,SRX26812020,SRS23296669,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 2,,strain:Tpfel long fin|age:3 dpf|collection date:2022 02|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 2,srrm4[y712] wild type replicate 2,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt2.pass2Aligned.sortedByCoord.out.bam,bam,22698373371.0,113599687.0,25938 wt2.pass2Aligned.sortedByCoord.out.bam,0:100.18 1:100.12,A:6063922145;C:5275724786;G:5212055837;T:6145709475;N:961128,100,100,,,6063922145,5275724786,5212055837,6145709475,961128,SRX26812020,SRS23296669,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.96129,0.96063,0.1003,0.09861,0.65744,0.65748,0.46167,0.46817,98,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34196,SRR31443232,SRX26812019,SRS23296667,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] mutant replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous mutant|Replicate:mutant 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] mutant replicate 1,srrm4[y712] mutant replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_mut.pass2Aligned.sortedByCoord.out.bam,bam,11282501509.0,56702666.0,25938 mut.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.55,A:2764745971;C:2868447715;G:2856237429;T:2792914545;N:155849,99,99,,,2764745971,2868447715,2856237429,2792914545,155849,SRX26812019,SRS23296667,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34197,SRR31443233,SRX26812018,SRS23296668,SRP546978,PRJNA1189474,Bulk RNA Seq of srrm4 homozygous mutant and wild type sibling larvae at 3 dpf,PRJNA1189474,Other,The goal of this project is to assess the effects of mutations in zebrafish srrm4 on alternative splicing of microexons. Homozygous mutant and homozygous wild type sibling larvae were identified from heterozygous parent crosses  Total RNA was isolated for sequencing at 3 dpf,,,,,srrm4[y712] wild type replicate 1,,strain:Tpfel long fin|age:3 dpf|collection date:2021 06|geo loc name:USA: Bethesda|sex:not applicable|tissue:head and torso|genotype:homozygous wild type|Replicate:wild type 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish larvae,srrm4[y712] wild type replicate 1,srrm4[y712] wild type replicate 1,TruSeq library,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP546978,,assembly:GRCz11,25938_wt.pass2Aligned.sortedByCoord.out.bam,bam,16346812838.0,82104499.0,25938 wt.pass2Aligned.sortedByCoord.out.bam,0:99.65 1:99.56,A:3996717287;C:4167381503;G:4130586142;T:4051899914;N:227992,99,99,,,3996717287,4167381503,4130586142,4051899914,227992,SRX26812018,SRS23296668,SRA2019780,Eunice Kennedy Shriver National Institute of Child Health and Human Development|Division of Developmental Biology,Eunice Kennedy Shriver National Institute of Child Health and Human Development,2,0.97776,0.97907,0.04095,0.04006,0.6702,0.67034,0.46611,0.46144,99,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,trueseq,bulk,bulk,bulk,,United States,2024-11-22,Larval,Larval,Head,Nervous System
34487,SRR31790708,SRX27151927,SRS23606412,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 2,GSM8695646,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695646,GSM8695646: RNA zebrafish larvae treated PM2.5 rep 2; Danio rerio; RNA Seq,GSM8695646 r1,GSM8695646,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_2_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_2_R2.fq.gz,fastq fastq,6499686900.0,21665623.0,GSM8695646 r1,0:150 1:150,A:1738791948;C:1515807515;G:1516684626;T:1724651740;N:3751071,150,150,,,1738791948,1515807515,1516684626,1724651740,3751071,SRX27151927,SRS23606412,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34488,SRR31790709,SRX27151926,SRS23606411,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 1,GSM8695645,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 1,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695645,GSM8695645: RNA zebrafish larvae treated PM2.5 rep 1; Danio rerio; RNA Seq,GSM8695645 r1,GSM8695645,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_1_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_1_R2.fq.gz,fastq fastq,10116536700.0,33721789.0,GSM8695645 r1,0:150 1:150,A:2712593040;C:2357036246;G:2349793342;T:2687696916;N:9417156,150,150,,,2712593040,2357036246,2349793342,2687696916,9417156,SRX27151926,SRS23606411,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34489,SRR31790710,SRX27151925,SRS23606410,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae control rep 2,GSM8695644,,source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing,RNA zebrafish larvae control rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:control,GSM8695644,GSM8695644: RNA zebrafish larvae control rep 2; Danio rerio; RNA Seq,GSM8695644 r1,GSM8695644,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_control_rep_2_R1.fq.gz RNA_zebrafish_larvae_control_rep_2_R2.fq.gz,fastq fastq,6347285700.0,21157619.0,GSM8695644 r1,0:150 1:150,A:1687168204;C:1494146408;G:1490096893;T:1672074832;N:3799363,150,150,,,1687168204,1494146408,1490096893,1672074832,3799363,SRX27151925,SRS23606410,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined